schrodinger.application.msv.gui.homology_modeling.hm_models module

parameters models for homology modeling

schrodinger.application.msv.gui.homology_modeling.hm_models.get_seq_display_name(seq)[source]

Formats sequence name and chain (if set) for display

class schrodinger.application.msv.gui.homology_modeling.hm_models.InputConfigAdapter[source]

Bases: schrodinger.models.adapters.inputconfig.ParamToInputConfig

STRING_BOOL_KWDS = ['build_deletions', 'build_insertions', 'build_transitions', 'keep_rotamers', 'minimize', 'side_opt', 'template_residue_numbers']
classmethod convert(param, destination_obj=None)

Copy data from the compound param to the destination object.

If no destination object is supplied, an empty one will be created.

Parameters
Returns

Destination object containing data from the compound param

Return type

object

class schrodinger.application.msv.gui.homology_modeling.hm_models.EmptyPrimeConfig(kw=None)[source]

Bases: schrodinger.application.prime.wrapper.PrimeConfig

Remove the spec from PrimeConfig.

The spec contains keys that can only be passed once in the input file, but TEMPLATE_NAME must be present in the input file for each template structure. Therefore, we create a new EmptyPrimeConfig object for each template and append them to the same input file.

specs = []
validateValues(*args, **kwargs)[source]

No-op to prevent traceback due to empty spec

__contains__(key, /)

True if the dictionary has the specified key, else False.

__init__(kw=None)

Accepts one argument which is either a path or a keyword dictionary.

__len__()

Return len(self).

as_bool(key)

Accepts a key as input. The corresponding value must be a string or the objects (True or 1) or (False or 0). We allow 0 and 1 to retain compatibility with Python 2.2.

If the string is one of True, On, Yes, or 1 it returns True.

If the string is one of False, Off, No, or 0 it returns False.

as_bool is not case sensitive.

Any other input will raise a ValueError.

>>> a = ConfigObj()
>>> a['a'] = 'fish'
>>> a.as_bool('a')
Traceback (most recent call last):
ValueError: Value "fish" is neither True nor False
>>> a['b'] = 'True'
>>> a.as_bool('b')
1
>>> a['b'] = 'off'
>>> a.as_bool('b')
0
as_float(key)

A convenience method which coerces the specified value to a float.

If the value is an invalid literal for float, a ValueError will be raised.

>>> a = ConfigObj()
>>> a['a'] = 'fish'
>>> a.as_float('a')  
Traceback (most recent call last):
ValueError: invalid literal for float(): fish
>>> a['b'] = '1'
>>> a.as_float('b')
1.0
>>> a['b'] = '3.2'
>>> a.as_float('b')  
3.2...
as_int(key)

A convenience method which coerces the specified value to an integer.

If the value is an invalid literal for int, a ValueError will be raised.

>>> a = ConfigObj()
>>> a['a'] = 'fish'
>>> a.as_int('a')
Traceback (most recent call last):
ValueError: invalid literal for int() with base 10: 'fish'
>>> a['b'] = '1'
>>> a.as_int('b')
1
>>> a['b'] = '3.2'
>>> a.as_int('b')
Traceback (most recent call last):
ValueError: invalid literal for int() with base 10: '3.2'
as_list(key)

A convenience method which fetches the specified value, guaranteeing that it is a list.

>>> a = ConfigObj()
>>> a['a'] = 1
>>> a.as_list('a')
[1]
>>> a['a'] = (1,)
>>> a.as_list('a')
[1]
>>> a['a'] = [1]
>>> a.as_list('a')
[1]
clear()

A version of clear that also affects scalars/sections Also clears comments and configspec.

Leaves other attributes alone :

depth/main/parent are not affected

copy() → a shallow copy of D
dict()

Return a deepcopy of self as a dictionary.

All members that are Section instances are recursively turned to ordinary dictionaries - by calling their dict method.

>>> n = a.dict()
>>> n == a
1
>>> n is a
0
fromkeys(value=None, /)

Create a new dictionary with keys from iterable and values set to value.

get(key, default=None)

A version of get that doesn’t bypass string interpolation.

getSpecsString()

Return a string of specifications. One keywords per line. Raises ValueError if this class has no specifications.

items() → list of D’s (key, value) pairs, as 2-tuples
iteritems() → an iterator over the (key, value) items of D
iterkeys() → an iterator over the keys of D
itervalues() → an iterator over the values of D
keys() → list of D’s keys
merge(indict)

A recursive update - useful for merging config files.

>>> a = '''[section1]
...     option1 = True
...     [[subsection]]
...     more_options = False
...     # end of file'''.splitlines()
>>> b = '''# File is user.ini
...     [section1]
...     option1 = False
...     # end of file'''.splitlines()
>>> c1 = ConfigObj(b)
>>> c2 = ConfigObj(a)
>>> c2.merge(c1)
>>> c2
ConfigObj({'section1': {'option1': 'False', 'subsection': {'more_options': 'False'}}})
pop(key, default=<object object>)

‘D.pop(k[,d]) -> v, remove specified key and return the corresponding value. If key is not found, d is returned if given, otherwise KeyError is raised’

popitem()

Pops the first (key,val)

printout()

Print all keywords of this instance to stdout.

This method is meant for debugging purposes.

reload()

Reload a ConfigObj from file.

This method raises a ReloadError if the ConfigObj doesn’t have a filename attribute pointing to a file.

rename(oldkey, newkey)

Change a keyname to another, without changing position in sequence.

Implemented so that transformations can be made on keys, as well as on values. (used by encode and decode)

Also renames comments.

reset()

Clear ConfigObj instance and restore to ‘freshly created’ state.

restore_default(key)

Restore (and return) default value for the specified key.

This method will only work for a ConfigObj that was created with a configspec and has been validated.

If there is no default value for this key, KeyError is raised.

restore_defaults()

Recursively restore default values to all members that have them.

This method will only work for a ConfigObj that was created with a configspec and has been validated.

It doesn’t delete or modify entries without default values.

setAlignment(alignment, ligands=('all'), include_water=False, template_number=1)
Parameters

  • alignment (BasePrimeAlignment) – Alignment.

  • ligands (tuple of str) – Names of ligands to be included in the model.

  • include_water (bool) – Whether to include water molecules in the built model.

  • template_number (int) – Template number

setdefault(key, default=None)

A version of setdefault that sets sequence if appropriate.

update(indict)

A version of update that uses our __setitem__.

validate(validator, preserve_errors=False, copy=False, section=None)

Test the ConfigObj against a configspec.

It uses the validator object from validate.py.

To run validate on the current ConfigObj, call:

test = config.validate(validator)

(Normally having previously passed in the configspec when the ConfigObj was created - you can dynamically assign a dictionary of checks to the configspec attribute of a section though).

It returns True if everything passes, or a dictionary of pass/fails (True/False). If every member of a subsection passes, it will just have the value True. (It also returns False if all members fail).

In addition, it converts the values from strings to their native types if their checks pass (and stringify is set).

If preserve_errors is True (False is default) then instead of a marking a fail with a False, it will preserve the actual exception object. This can contain info about the reason for failure. For example the VdtValueTooSmallError indicates that the value supplied was too small. If a value (or section) is missing it will still be marked as False.

You must have the validate module to use preserve_errors=True.

You can then use the flatten_errors function to turn your nested results dictionary into a flattened list of failures - useful for displaying meaningful error messages.

values() → list of D’s values
walk(function, raise_errors=True, call_on_sections=False, **keywargs)

Walk every member and call a function on the keyword and value.

Return a dictionary of the return values

If the function raises an exception, raise the errror unless raise_errors=False, in which case set the return value to False.

Any unrecognised keyword arguments you pass to walk, will be pased on to the function you pass in.

Note: if call_on_sections is True then - on encountering a subsection, first the function is called for the whole subsection, and then recurses into it’s members. This means your function must be able to handle strings, dictionaries and lists. This allows you to change the key of subsections as well as for ordinary members. The return value when called on the whole subsection has to be discarded.

See the encode and decode methods for examples, including functions.

caution

You can use walk to transform the names of members of a section but you mustn’t add or delete members.

>>> config = '''[XXXXsection]
... XXXXkey = XXXXvalue'''.splitlines()
>>> cfg = ConfigObj(config)
>>> cfg
ConfigObj({'XXXXsection': {'XXXXkey': 'XXXXvalue'}})
>>> def transform(section, key):
...     val = section[key]
...     newkey = key.replace('XXXX', 'CLIENT1')
...     section.rename(key, newkey)
...     if isinstance(val, (tuple, list, dict)):
...         pass
...     else:
...         val = val.replace('XXXX', 'CLIENT1')
...         section[newkey] = val
>>> cfg.walk(transform, call_on_sections=True)
{'CLIENT1section': {'CLIENT1key': None}}
>>> cfg
ConfigObj({'CLIENT1section': {'CLIENT1key': 'CLIENT1value'}})
write(outfile=None, section=None)

Write the current ConfigObj as a file

tekNico: FIXME: use StringIO instead of real files

>>> filename = a.filename
>>> a.filename = 'test.ini'
>>> a.write()
>>> a.filename = filename
>>> a == ConfigObj('test.ini', raise_errors=True)
1
>>> import os
>>> os.remove('test.ini')
writeConfig(filename)

Writes a simplified input file to filename.

This input file needs to be run via $SCHRODINGER/prime.

Parameters

filename (str) – Name of output file.

writeInputFile(filename, ignore_none=False, yesno=False, smartsort=False)

Write the configuration to a file in the InputConfig format.

Parameters

  • filename (a file path or an open file handle) – The file to write the configuration to.

  • ignore_none (bool) – If True, keywords with a value of None will not be written to the input file.

  • yesno (bool) – If True, boolean keywords will be written as “yes” and “no”, if False, as “True” and “False”.

  • smartsort (bool) – If True, keywords that are identical except for the numbers at the end will be sorted such that “2” will go before “10”.

class schrodinger.application.msv.gui.homology_modeling.hm_models.Ligand(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

Parameters

  • name – Unique ligand name including chain and residue number

  • pdbres – Ligand residue name

  • chain – Ligand chain name

  • resnum – Ligand residue number

  • molnum – Ligand molecule number

  • asl – ASL representing the ligand

  • structure_name – Name of the structure (excluding chain)

  • cofactor – Whether the het is not a ligand as defined by the ligand preferences

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
pdbres: 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
chain: 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
resnum: 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
molnum: 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
asl: 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
structure_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
cofactor: 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
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)

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

classmethod addSubParam(name, param, update_owner=True)
aslChanged
aslReplaced
blockSignals(self, bool) → bool
block_signal_propagation()
chainChanged
chainReplaced
childEvent(self, QChildEvent)
children(self) → List[QObject]
cofactorChanged
cofactorReplaced
classmethod configureParam()

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

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

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

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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(*args, **kwargs)
classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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, 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, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

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

objectNameChanged(self, 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
pdbresChanged
pdbresReplaced
property(self, str) → Any
pyqtConfigure(...)

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

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

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
structure_nameChanged
structure_nameReplaced
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str
valueChanged
class schrodinger.application.msv.gui.homology_modeling.hm_models.LigandMolecule(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

Ligand for display (combines ligands with the same molnum)

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
structure_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
source_ligands: list

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.

property cofactor
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)

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

classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

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

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

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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(*args, **kwargs)
classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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, 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, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

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

objectNameChanged(self, 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, str) → Any
pyqtConfigure(...)

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

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

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
source_ligandsChanged
source_ligandsReplaced
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
structure_nameChanged
structure_nameReplaced
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str
valueChanged
class schrodinger.application.msv.gui.homology_modeling.hm_models.LigandConstraint(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

res: schrodinger.protein.residue.Residue

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
ligname: 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
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)

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

classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

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

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

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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(*args, **kwargs)
classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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, 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, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
lignameChanged
lignameReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, 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, str) → Any
pyqtConfigure(...)

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

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

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str
valueChanged
class schrodinger.application.msv.gui.homology_modeling.hm_models.TargetTemplatePair(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

target_seq: schrodinger.protein.sequence.ProteinSequence

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
template_seq: schrodinger.protein.sequence.ProteinSequence

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
identity: 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
ligands: List[schrodinger.application.msv.gui.homology_modeling.hm_models.Ligand]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

__init__(*args, **kwargs)[source]

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

property is_valid

Whether both the target and template are defined

property has_waters

Whether the template structure has waters :rtype: bool

property alignment_quality
updateIdentity()[source]
getPrimeTemplateName(suffix=None)[source]

Get the name that will be used to identify this prime template.

Parameters

suffix (int or NoneType) – Optional suffix for alignment name (needed if more than one target uses the same template)

writeInputForPrime(taskdir, suffix=None)[source]

Convert the sequences into prime format and write them to file.

Parameters

suffix (int or NoneType) – Optional suffix for alignment name (needed if more than one target uses the same template)

Returns

Prime alignment

Return type

schrodinger.application.prime.wrapper.BasePrimeAlignment

writeInputForConsensus(file_name, append=False)[source]

Convert the sequences into prime format and write them to file.

Parameters

  • file_name (str) – Alignment file name to write (absolute path)

  • append (bool) – Whether to create a new alignment file or append

Returns

Prime alignment

Return type

schrodinger.application.prime.wrapper.BasePrimeAlignment

getSelectedLigandsForPair(all_selected_ligands)[source]

Get the names of the selected ligands belonging to this pair

Parameters

all_selected_ligands (collections.iterable(Ligand)) – Selected ligands across all pairs

Return type

list[Ligand]

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
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

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

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

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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(*args, **kwargs)
classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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.

identityChanged
identityReplaced
inherits(self, 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, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
ligandsChanged
ligandsReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, 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, str) → Any
pyqtConfigure(...)

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

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

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
target_seqChanged
target_seqReplaced
template_seqChanged
template_seqReplaced
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str
valueChanged
class schrodinger.application.msv.gui.homology_modeling.hm_models.LigandDialogModel(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

ligands: List[schrodinger.application.msv.gui.homology_modeling.hm_models.LigandMolecule]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

selected_ligands: List[schrodinger.application.msv.gui.homology_modeling.hm_models.LigandMolecule]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

has_waters: 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
include_waters: 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
constrain_ligand: 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
ligand_constraints: List[schrodinger.application.msv.gui.homology_modeling.hm_models.LigandConstraint]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

pick_ligand: 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
classmethod getJsonBlacklist()[source]

@overrides: tasks.AbstractCmdTask

getSelectedLigands()[source]
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)

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

classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

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

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

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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(*args, **kwargs)
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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.

has_watersChanged
has_watersReplaced
include_watersChanged
include_watersReplaced
inherits(self, 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, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
ligand_constraintsChanged
ligand_constraintsReplaced
ligandsChanged
ligandsReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, 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
pick_ligandChanged
pick_ligandReplaced
property(self, str) → Any
pyqtConfigure(...)

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

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

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str
valueChanged
class schrodinger.application.msv.gui.homology_modeling.hm_models.PrimeSettings(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

Homology settings that are written to the prime input file

prime_method: schrodinger.application.msv.gui.homology_modeling.constants.PrimeMethod
build_deletions: 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
build_insertions: 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
build_transitions: 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
keep_rotamers: 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
max_insertion_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
minimize: 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_output_struct: 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
side_opt: 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
template_residue_numbers: 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
getSummaryText()[source]

Get a string summarizing the settings.

Prime method and the number of output structures will be shown; all other options will be grouped under custom or default.

initConcrete()[source]

Override to customize initialization of concrete params.

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)

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

classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
build_deletionsChanged
build_deletionsReplaced
build_insertionsChanged
build_insertionsReplaced
build_transitionsChanged
build_transitionsReplaced
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

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

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

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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(*args, **kwargs)
classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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, str) → bool
initAbstract()
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, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
keep_rotamersChanged
keep_rotamersReplaced
killTimer(self, int)
max_insertion_sizeChanged
max_insertion_sizeReplaced
metaObject(self) → QMetaObject
minimizeChanged
minimizeReplaced
moveToThread(self, QThread)
num_output_structChanged
num_output_structReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, 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
prime_methodChanged
prime_methodReplaced
property(self, str) → Any
pyqtConfigure(...)

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

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

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
side_optChanged
side_optReplaced
signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
template_residue_numbersChanged
template_residue_numbersReplaced
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str
valueChanged
class schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingSettings(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

prime_settings: schrodinger.application.msv.gui.homology_modeling.hm_models.PrimeSettings

Homology settings that are written to the prime input file

include_hets: 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
add_residue_labels: 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
ligand_dlg_model: schrodinger.application.msv.gui.homology_modeling.hm_models.LigandDialogModel
set_constraints: 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
proximity_constraints: List

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.

pick_proximity: 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
initConcrete()[source]

Override to customize initialization of concrete params.

classmethod getJsonBlacklist()[source]

@overrides: tasks.AbstractCmdTask

classmethod adapter49009(json_dict)[source]
classmethod adapter51105(json_dict)[source]
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)

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

classmethod addSubParam(name, param, update_owner=True)
add_residue_labelsChanged
add_residue_labelsReplaced
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

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

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

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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(*args, **kwargs)
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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.

include_hetsChanged
include_hetsReplaced
inherits(self, str) → bool
initAbstract()
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, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
ligand_dlg_modelChanged
ligand_dlg_modelReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, 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
pick_proximityChanged
pick_proximityReplaced
prime_settingsChanged
prime_settingsReplaced
property(self, str) → Any
proximity_constraintsChanged
proximity_constraintsReplaced
pyqtConfigure(...)

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

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

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
set_constraintsChanged
set_constraintsReplaced
signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str
valueChanged
class schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingInput(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

mode: schrodinger.application.msv.gui.homology_modeling.constants.Mode
heteromultimer_mode: schrodinger.application.msv.gui.homology_modeling.constants.HeteromultimerMode
target_template_pairs: List[schrodinger.application.msv.gui.homology_modeling.hm_models.TargetTemplatePair]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

composite_regions: list

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.

pick_chimera: 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
ready: 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
settings: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingSettings
composite_residues

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__(*args, **kwargs)[source]

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

classmethod getJsonBlacklist()[source]

@overrides: tasks.AbstractCmdTask

classmethod adapter51082(json_dict)[source]
getMinAlignmentQuality()[source]
Returns

The minimum alignment quality of all alignment pairs or None if no alignment pairs exist

Return type

constants.AlignmentQuality or NoneType

hasGaps()[source]
Returns

Whether any of the pairs have gaps

Return type

bool

getNumRegions()[source]
Returns

The number of chimeric regions

Return type

int

getCompositeArray()[source]
Returns

Composite array specifying 1-based template number for each target position and the pairs used in the array

Return type

str, list[TargetTemplatePair]

updateHomologyStatus()[source]

Update aln homology status to reflect the current target template pairs

getSeqsToAlign()[source]

Get sequences for sequence alignment

getSeqsToStructureAlign()[source]

Get sequences for structure alignment

getLigandAndWaterSettings()[source]

Get all selected ligands and whether the Prime job should include water molecules.

Returns

A tuple of - A list of all selected ligands - Whether waters should be included

Return type

tuple(list[Ligand], bool)

isChimera()[source]
usesLigands()[source]

Return whether the mode can use ligands (regardless of whether ligands are present)

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
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
composite_regionsChanged
composite_regionsReplaced
classmethod configureParam()

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

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

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

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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(*args, **kwargs)
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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.

heteromultimer_modeChanged
heteromultimer_modeReplaced
inherits(self, 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, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
metaObject(self) → QMetaObject
modeChanged
modeReplaced
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, 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
pick_chimeraChanged
pick_chimeraReplaced
property(self, str) → Any
pyqtConfigure(...)

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

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

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
settingsChanged
settingsReplaced
signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
target_template_pairsChanged
target_template_pairsReplaced
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str
valueChanged
class schrodinger.application.msv.gui.homology_modeling.hm_models.HMLauncherTask(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.tasks.jobtasks._AbstractJobMixin, schrodinger.tasks.tasks.SignalTask

Task to launch homology modeling jobtasks.

Inherits from jobtasks._AbstractJobMixin to get jobtasks.is_jobtask to return True, but does not run a job directly.

job_config: schrodinger.tasks.jobtasks.JobConfig
subtask: schrodinger.tasks.tasks.AbstractTask
setUpMain()[source]
write(skip_preprocessing=False)[source]
AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
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
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
property PROGRAM_NAME
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, **kwargs)

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

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

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

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

Parameters

  • func – the function to add

  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

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

Parameters

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

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

addPreprocessor(func, order=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)
blockSignals(self, bool) → bool
block_signal_propagation()
calling_context

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
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

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

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
failure_info

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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

static guard_method(func)
inWriteMode()
inherits(self, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: paramters.CompoundParam

input: schrodinger.models.parameters.CompoundParam

All `CompoundParam`s are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

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

@overrides: tasks.AbstractTask

killTimer(self, int)
mainDone
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, 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, str) [signal]

output: schrodinger.models.parameters.CompoundParam

All `CompoundParam`s are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

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

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

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

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

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

classmethod paramName()

Get the name of the param:

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

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
postprocessors()
Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()
Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

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

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

Parameters

  • chain (FuncChainDecorator) – which chain to process

  • result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: 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, str) → Any
pyqtConfigure(...)

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

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

@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)
run()
runCmd(cmd)

@overrides: tasks.AbstractCmdTask

classmethod runFromCmdLine()

@overrides: tasks.AbstractTask

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

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

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
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

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

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

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

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

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

Parameters

taskdir_spec – one of the four options listed above

start(skip_preprocessing=False)

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

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

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

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

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

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

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

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.

writeStuZipFile()
class schrodinger.application.msv.gui.homology_modeling.hm_models.BasePrimeTask(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.tasks.jobtasks.CmdJobTask

Task that runs prime on self.input_files. Caller is responsible for writing and setting self.input_files.

input_files: 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.

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
job_config: schrodinger.tasks.jobtasks.JobConfig
initConcrete()[source]

Override to customize initialization of concrete params.

makeCmd()[source]

@overrides: tasks.AbstractCmdTask

AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
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
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
property PROGRAM_NAME
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, cmd_list=None, **kwargs)

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

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

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

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

Parameters

  • func – the function to add

  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

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

Parameters

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

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

addPreprocessor(func, order=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)
blockSignals(self, bool) → bool
block_signal_propagation()
calling_context

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
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

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

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
failure_info

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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, str) → bool
initAbstract()
initializeValue()

@overrides: paramters.CompoundParam

input: schrodinger.models.parameters.CompoundParam

All `CompoundParam`s are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
inputChanged
inputReplaced
input_filesChanged
input_filesReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

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

@overrides: tasks.AbstractTask

killTimer(self, int)
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, 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, str) [signal]

output: schrodinger.models.parameters.CompoundParam

All `CompoundParam`s are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
outputChanged
outputReplaced
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
postprocessors()
Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()
Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

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

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

Parameters

  • chain (FuncChainDecorator) – which chain to process

  • result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: 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, str) → Any
pyqtConfigure(...)

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

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

@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)
run()
runCmd(cmd)

@overrides: tasks.AbstractCmdTask

classmethod runFromCmdLine()

@overrides: tasks.AbstractTask

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

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

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
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

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

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

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

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

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

Parameters

taskdir_spec – one of the four options listed above

start(skip_preprocessing=False)

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

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

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

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

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

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

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

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.application.msv.gui.homology_modeling.hm_models.BaseHomologyTaskMixin[source]

Bases: schrodinger.models.parameters.CompoundParamMixin

Mixin with shared methods for all homology modeling tasks

Subclasses must inherit from a Task class and define the appropriate task methods (e.g. makeCmd/mainFunction, preprocessors).

aln

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
input: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingInput
output_file: schrodinger.tasks.tasks.TaskFile
initializeValue()[source]
initConcrete()[source]
getOutputStructureFiles()[source]

Get the task’s output structure file(s).

class schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyTaskMixin[source]

Bases: schrodinger.application.msv.gui.homology_modeling.hm_models.BaseHomologyTaskMixin

Mixin with shared methods for simple homology modeling tasks.

Subclasses must inherit from a Task class and define the appropriate task methods (e.g. makeCmd/mainFunction, preprocessors).

file_prefix

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
initConcrete()[source]
aln

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
getOutputStructureFiles()

Get the task’s output structure file(s).

initializeValue()
input: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingInput
output_file: schrodinger.tasks.tasks.TaskFile
class schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingTask(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyTaskMixin, schrodinger.application.msv.gui.homology_modeling.hm_models.BasePrimeTask

ENTRY_TITLE_FMT = 'Model of {target} based on {templates}'
AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
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
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
property PROGRAM_NAME
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, cmd_list=None, **kwargs)

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

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

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

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

Parameters

  • func – the function to add

  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

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

Parameters

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

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

addPreprocessor(func, order=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)
aln

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
blockSignals(self, bool) → bool
block_signal_propagation()
calling_context

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
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

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

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
failure_info

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
file_prefix

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

getOutputStructureFiles()

Get the task’s output structure file(s).

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: paramters.CompoundParam

input: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingInput
inputChanged
inputReplaced
input_files: 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.

input_filesChanged
input_filesReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
job_config: schrodinger.tasks.jobtasks.JobConfig
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
kill()

@overrides: tasks.AbstractTask

killTimer(self, int)
makeCmd()

@overrides: tasks.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, 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, str) [signal]

output: schrodinger.models.parameters.CompoundParam

All `CompoundParam`s are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
outputChanged
outputReplaced
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
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
postprocessors()
Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()
Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

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

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

Parameters

  • chain (FuncChainDecorator) – which chain to process

  • result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: 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, str) → Any
pyqtConfigure(...)

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

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

@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)
run()
runCmd(cmd)

@overrides: tasks.AbstractCmdTask

classmethod runFromCmdLine()

@overrides: tasks.AbstractTask

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

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

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
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

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

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

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

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

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

Parameters

taskdir_spec – one of the four options listed above

start(skip_preprocessing=False)

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

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

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

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

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

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

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

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.application.msv.gui.homology_modeling.hm_models.ChimeraHomologyModelingTask(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingTask

ENTRY_TITLE_FMT = 'Chimeric model of {target} based on {templates}'
AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
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
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
property PROGRAM_NAME
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, cmd_list=None, **kwargs)

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

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

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

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

Parameters

  • func – the function to add

  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

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

Parameters

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

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

addPreprocessor(func, order=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)
aln

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
blockSignals(self, bool) → bool
block_signal_propagation()
calling_context

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
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

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

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
failure_info

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
file_prefix

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

getOutputStructureFiles()

Get the task’s output structure file(s).

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: paramters.CompoundParam

input: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingInput
inputChanged
inputReplaced
input_files: 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.

input_filesChanged
input_filesReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
job_config: schrodinger.tasks.jobtasks.JobConfig
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
kill()

@overrides: tasks.AbstractTask

killTimer(self, int)
makeCmd()

@overrides: tasks.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, 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, str) [signal]

output: schrodinger.models.parameters.CompoundParam

All `CompoundParam`s are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
outputChanged
outputReplaced
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
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
postprocessors()
Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()
Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

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

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

Parameters

  • chain (FuncChainDecorator) – which chain to process

  • result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: 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, str) → Any
pyqtConfigure(...)

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

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

@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)
run()
runCmd(cmd)

@overrides: tasks.AbstractCmdTask

classmethod runFromCmdLine()

@overrides: tasks.AbstractTask

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

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

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
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

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

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

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

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

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

Parameters

taskdir_spec – one of the four options listed above

start(skip_preprocessing=False)

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

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

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

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

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

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

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

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.application.msv.gui.homology_modeling.hm_models.HeteromultimerHomologyModelingTask(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.application.msv.gui.homology_modeling.hm_models.BaseHomologyTaskMixin, schrodinger.application.msv.gui.homology_modeling.hm_models.BasePrimeTask

class Input(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

settings: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingSettings
input_list: List[schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingInput]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

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)

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

classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

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

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

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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(*args, **kwargs)
classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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, 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.

input_listChanged
input_listReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

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

objectNameChanged(self, 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, str) → Any
pyqtConfigure(...)

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

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

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
settingsChanged
settingsReplaced
signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str
valueChanged
AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
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
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
property PROGRAM_NAME
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, cmd_list=None, **kwargs)

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

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

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

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

Parameters

  • func – the function to add

  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

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

Parameters

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

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

addPreprocessor(func, order=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)
aln

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
blockSignals(self, bool) → bool
block_signal_propagation()
calling_context

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
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

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

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
failure_info

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

getOutputStructureFiles()

Get the task’s output structure file(s).

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: paramters.CompoundParam

input: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingInput
inputChanged
inputReplaced
input_files: 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.

input_filesChanged
input_filesReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
job_config: schrodinger.tasks.jobtasks.JobConfig
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
kill()

@overrides: tasks.AbstractTask

killTimer(self, int)
makeCmd()

@overrides: tasks.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, 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, str) [signal]

output: schrodinger.models.parameters.CompoundParam

All `CompoundParam`s are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
outputChanged
outputReplaced
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
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
postprocessors()
Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()
Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

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

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

Parameters

  • chain (FuncChainDecorator) – which chain to process

  • result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: 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, str) → Any
pyqtConfigure(...)

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

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

@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)
run()
runCmd(cmd)

@overrides: tasks.AbstractCmdTask

classmethod runFromCmdLine()

@overrides: tasks.AbstractTask

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

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

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
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

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

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

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

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

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

Parameters

taskdir_spec – one of the four options listed above

start(skip_preprocessing=False)

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

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

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

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

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

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

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

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.application.msv.gui.homology_modeling.hm_models.BatchHomologyModelingTask(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyTaskMixin, schrodinger.tasks.jobtasks.ComboJobTask

job_config: schrodinger.tasks.jobtasks.JobConfig
class Input(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingInput

Variables

prime_input_files – List of prime .inp files

prime_input_files: 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__(*args, **kwargs)

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

classmethod adapter51082(json_dict)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
composite_regions: list

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.

composite_regionsChanged
composite_regionsReplaced
composite_residues

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

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

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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(*args, **kwargs)
getCompositeArray()
Returns

Composite array specifying 1-based template number for each target position and the pairs used in the array

Return type

str, list[TargetTemplatePair]

classmethod getJsonBlacklist()

@overrides: tasks.AbstractCmdTask

getLigandAndWaterSettings()

Get all selected ligands and whether the Prime job should include water molecules.

Returns

A tuple of - A list of all selected ligands - Whether waters should be included

Return type

tuple(list[Ligand], bool)

getMinAlignmentQuality()
Returns

The minimum alignment quality of all alignment pairs or None if no alignment pairs exist

Return type

constants.AlignmentQuality or NoneType

getNumRegions()
Returns

The number of chimeric regions

Return type

int

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
getSeqsToAlign()

Get sequences for sequence alignment

getSeqsToStructureAlign()

Get sequences for structure alignment

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.

hasGaps()
Returns

Whether any of the pairs have gaps

Return type

bool

heteromultimer_mode: schrodinger.application.msv.gui.homology_modeling.constants.HeteromultimerMode
heteromultimer_modeChanged
heteromultimer_modeReplaced
inherits(self, 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, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isChimera()
isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
metaObject(self) → QMetaObject
mode: schrodinger.application.msv.gui.homology_modeling.constants.Mode
modeChanged
modeReplaced
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, 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
pick_chimera: 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
pick_chimeraChanged
pick_chimeraReplaced
prime_input_filesChanged
prime_input_filesReplaced
property(self, str) → Any
pyqtConfigure(...)

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

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

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
settings: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingSettings
settingsChanged
settingsReplaced
signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
target_template_pairs: List[schrodinger.application.msv.gui.homology_modeling.hm_models.TargetTemplatePair]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

target_template_pairsChanged
target_template_pairsReplaced
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

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

Update aln homology status to reflect the current target template pairs

usesLigands()

Return whether the mode can use ligands (regardless of whether ligands are present)

valueChanged
ENTRY_TITLE_FMT = 'Model of {target} based on {template}'
initializeValue()[source]

@overrides: paramters.CompoundParam

getOutputStructureFiles()[source]

@overrides: HomologyTaskMixin

mainFunction()[source]
AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
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 = <object object>
WAITING = 0
__init__(*args, **kwargs)

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

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

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

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

Parameters

  • func – the function to add

  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addInputDirectory(directory)

Add an input directory to be copied over with the job.

addInputFile(filename)

Register the given file with job control as an input file, so that it gets copied to the job directory when the task starts.

Parameters

filename (str) – Input file path.

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

addOutputFile(filename)

Register the given file with job control as an output file, so that it gets copied to the launch directory after the tasks completes.

Parameters

filename (str) – Input file path.

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)
aln

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
backendMain()
blockSignals(self, bool) → bool
block_signal_propagation()
calling_context

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
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

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

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
failure_info

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
file_prefix

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

getLogAsString()
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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()
incorporation_file: 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
incorporation_fileChanged
incorporation_fileReplaced
inherits(self, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

input: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingInput
Variables

prime_input_files – List of prime .inp files

inputChanged
inputReplaced
input_files: list

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.

input_filesChanged
input_filesReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

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

@overrides: tasks.AbstractCmdTask

Child classes must not override this method.

makeJobSpecFromCmd(cmd)
makeLaunchParams()
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, 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, str) [signal]

output: schrodinger.models.parameters.CompoundParam

All `CompoundParam`s are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
outputChanged
outputReplaced
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
output_fileChanged
output_fileReplaced
output_files: list

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.

output_filesChanged
output_filesReplaced
classmethod owner()

Get the owner of the param:

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

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

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

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

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

classmethod paramName()

Get the name of the param:

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

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
postprocessors()
Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()
Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

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

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

Parameters

  • chain (FuncChainDecorator) – which chain to process

  • result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: 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, str) → Any
pyqtConfigure(...)

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

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

@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)
run()
runBackend()

@overrides: AbstractComboTask

runCmd(cmd)

@overrides: tasks.AbstractCmdTask

classmethod runFromCmdLine()

@overrides: tasks.AbstractTask

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

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

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
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

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

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

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

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

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

Parameters

taskdir_spec – one of the four options listed above

start(*args, **kwargs)

@overrides: AbstractTask

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

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

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

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

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.

wrapCmdInLaunchApi(cmd)
write(skip_preprocessing=False)
writeJsonFile(filename)
writeStuZipFile()
class schrodinger.application.msv.gui.homology_modeling.hm_models.ConsensusHomologyModelingTask(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.application.msv.gui.homology_modeling.hm_models.BaseHomologyTaskMixin, schrodinger.tasks.jobtasks.CmdJobTask

input_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
job_config: schrodinger.tasks.jobtasks.JobConfig
makeCmd()[source]

@overrides: tasks.AbstractCmdTask

AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
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
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
property PROGRAM_NAME
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, cmd_list=None, **kwargs)

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

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

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

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

Parameters

  • func – the function to add

  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

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

Parameters

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

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

addPreprocessor(func, order=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)
aln

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
blockSignals(self, bool) → bool
block_signal_propagation()
calling_context

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
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

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

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
failure_info

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

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

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

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

classmethod fromJson(json_obj)

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

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

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

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

getOutputStructureFiles()

Get the task’s output structure file(s).

classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

Using the string name to 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, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: paramters.CompoundParam

input: schrodinger.application.msv.gui.homology_modeling.hm_models.HomologyModelingInput
inputChanged
inputReplaced
input_fileChanged
input_fileReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

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

@overrides: tasks.AbstractTask

killTimer(self, int)
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, 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, str) [signal]

output: schrodinger.models.parameters.CompoundParam

All `CompoundParam`s are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
outputChanged
outputReplaced
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
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
postprocessors()
Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()
Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

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

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

Parameters

  • chain (FuncChainDecorator) – which chain to process

  • result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: 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, str) → Any
pyqtConfigure(...)

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

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

@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)
run()
runCmd(cmd)

@overrides: tasks.AbstractCmdTask

classmethod runFromCmdLine()

@overrides: tasks.AbstractTask

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

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

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
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters

  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

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

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

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

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

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

Parameters

taskdir_spec – one of the four options listed above

start(skip_preprocessing=False)

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

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

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

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

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)

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

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

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

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()
schrodinger.application.msv.gui.homology_modeling.hm_models.get_possible_templates(aln)[source]

Generator for sequences from the given alignment that can be templates

Return type

collections.Iterable[sequence.ProteinSequence]

schrodinger.application.msv.gui.homology_modeling.hm_models.get_selected_nonref_seqs(aln)[source]

Generator for non-reference sequences from the given alignment that are selected (or all non-reference seqs if there is no selection)

Return type

collections.Iterable[sequence.ProteinSequence]

schrodinger.application.msv.gui.homology_modeling.hm_models.get_min_alignment_quality(pairs)[source]
Parameters

pairs (collections.iterable[TargetTemplatePair]) – Target template pairs

Returns

The minimum alignment quality of all alignment pairs or None if no alignment pairs exist

Return type

constants.AlignmentQuality or NoneType

schrodinger.application.msv.gui.homology_modeling.hm_models.get_task_from_model(gui_model)[source]
schrodinger.application.msv.gui.homology_modeling.hm_models.get_task(hm_input)[source]

Return a task for the specified input

schrodinger.application.msv.gui.homology_modeling.hm_models.get_task_class(mode)[source]