schrodinger.application.prepwizard2.diagnostics module¶
-
class
schrodinger.application.prepwizard2.diagnostics.
Problems
(*args, _param_type=<object object>, **kwargs)[source]¶ Bases:
schrodinger.models.parameters.CompoundParam
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invalid_types
: List[Tuple[int, int, int]]¶ 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.
-
missing
: List[Tuple[int, int, int, bool]]¶ 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.
-
overlapping
: List[Tuple[int, int]]¶ 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.
-
alternates
: List[Tuple[int, float]]¶ 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
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__init__
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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classmethod
addSubParam
(name, param, update_owner=True)¶
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alternatesChanged
¶
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alternatesReplaced
¶
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blockSignals
(self, bool) → bool¶
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block_signal_propagation
()¶
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childEvent
(self, QChildEvent)¶
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children
(self) → List[QObject]¶
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classmethod
configureParam
()¶ Override this class method to set up the abstract param class (e.g. setParamReference on child params.)
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connectNotify
(self, QMetaMethod)¶
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customEvent
(self, QEvent)¶
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classmethod
defaultValue
(*args, **kwargs)¶
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deleteLater
(self)¶
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destroyed
¶ destroyed(self, object: QObject = None) [signal]
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disconnect
(self)¶
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disconnectNotify
(self, QMetaMethod)¶
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dumpObjectInfo
(self)¶
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dumpObjectTree
(self)¶
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dynamicPropertyNames
(self) → List[QByteArray]¶
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event
(self, QEvent) → bool¶
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eventFilter
(self, QObject, QEvent) → bool¶
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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
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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]
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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
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classmethod
fromJsonImplementation
(json_dict)¶ Sets the value of this compound param value object from a JSON dict.
Warning
This should never be called directly.
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getAbstractParam
(*args, **kwargs)¶
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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
, notcls.coord.x
.
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classmethod
getParamSignal
(*args, **kwargs)¶
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classmethod
getParamValue
(*args, **kwargs)¶
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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.
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classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
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getTypeHint
()¶
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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.
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inherits
(self, str) → bool¶
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initAbstract
()¶
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initConcrete
()¶ Override to customize initialization of concrete params.
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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.
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installEventFilter
(self, QObject)¶
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invalid_typesChanged
¶
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invalid_typesReplaced
¶
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classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
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isDefault
(*args, **kwargs)¶
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isSignalConnected
(self, QMetaMethod) → bool¶
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isWidgetType
(self) → bool¶
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isWindowType
(self) → bool¶
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killTimer
(self, int)¶
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metaObject
(self) → QMetaObject¶
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missingChanged
¶
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missingReplaced
¶
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moveToThread
(self, QThread)¶
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objectName
(self) → str¶
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objectNameChanged
¶ objectNameChanged(self, str) [signal]
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overlappingChanged
¶
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overlappingReplaced
¶
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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
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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.
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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'
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parent
(self) → QObject¶
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property
(self, str) → Any¶
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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.
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receivers
(self, PYQT_SIGNAL) → int¶
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removeEventFilter
(self, QObject)¶
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reset
(*args, **kwargs)¶
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sender
(self) → QObject¶
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senderSignalIndex
(self) → int¶
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setObjectName
(self, str)¶
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classmethod
setParamValue
(*args, **kwargs)¶
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setParent
(self, QObject)¶
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setProperty
(self, str, Any) → bool¶
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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.
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setValue
(*args, **kwargs)¶
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signalsBlocked
(self) → bool¶
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skip_eq_check
()¶
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startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
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staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
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thread
(self) → QThread¶
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timerEvent
(self, QTimerEvent)¶
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toDict
(*args, **kwargs)¶
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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
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tr
(self, str, disambiguation: str = None, n: int = - 1) → str¶
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valueChanged
¶
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schrodinger.application.prepwizard2.diagnostics.
get_atoms_with_improper_atom_types
(st)[source]¶ Returns a list of (atomnum, expected_valence, actual_valence) items. expected_valence is None for atom types of 150 or above.
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schrodinger.application.prepwizard2.diagnostics.
find_missing_res_atoms
(st)[source]¶ Seaches the specified structure for missing residue atoms, and returns a list of: (atomnum, num_heavy, expected_heavy, missing_only_sidechains)
This list DOES include residues with only backbone atoms missing.
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schrodinger.application.prepwizard2.diagnostics.
find_residues_with_multiple_occupancies
(st)[source]¶ Find residues that have at least one atom with multiple occupancies (alternate states).
- Parameters
st (
structure.Structure
) – Protein structure- Returns
List of (Atom index, average occupancy)
- Return type
list