schrodinger.application.steps.dataclasses module

Data classes to be used as input/output objects for steps and their associated serializers which may be used when batching those steps.

exception schrodinger.application.steps.dataclasses.StepsError

Bases: RuntimeError

class schrodinger.application.steps.dataclasses.MolToSmilesSerializer

Bases: schrodinger.stepper.stepper.Serializer

A serializer using RDKit’s canonical SMILES of the Mol as the serialized form.

DataType

alias of rdkit.Chem.rdchem.Mol

deserialize(fname)

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

fromString(smiles_str)
toString(output_mol)
class schrodinger.application.steps.dataclasses.MolInMixin

Bases: object

Input

alias of rdkit.Chem.rdchem.Mol

InputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

class schrodinger.application.steps.dataclasses.MolOutMixin

Bases: object

Output

alias of rdkit.Chem.rdchem.Mol

OutputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

class schrodinger.application.steps.dataclasses.MolMolMixin

Bases: schrodinger.application.steps.dataclasses.MolInMixin, schrodinger.application.steps.dataclasses.MolOutMixin

class schrodinger.application.steps.dataclasses.ScoredMol(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

mol: rdkit.Chem.rdchem.Mol

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
score: 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
molChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

molReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

scoreChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

scoreReplaced

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

class schrodinger.application.steps.dataclasses.ScoredMolSerializer

Bases: schrodinger.stepper.stepper.Serializer

A serializer using RDKit’s canonical SMILES of the Mol and the score value string separated by a ‘,’ as the serialized form.

DataType

alias of schrodinger.application.steps.dataclasses.ScoredMol

SEPARATOR = ','
toString(scored_mol)
fromString(scored_mol_str)
class schrodinger.application.steps.dataclasses.ScoredMolInMixin

Bases: object

Input

alias of schrodinger.application.steps.dataclasses.ScoredMol

InputSerializer

alias of schrodinger.application.steps.dataclasses.ScoredMolSerializer

class schrodinger.application.steps.dataclasses.ScoredMolOutMixin

Bases: object

Output

alias of schrodinger.application.steps.dataclasses.ScoredMol

OutputSerializer

alias of schrodinger.application.steps.dataclasses.ScoredMolSerializer

class schrodinger.application.steps.dataclasses.ScorerMixin

Bases: object

Input

alias of rdkit.Chem.rdchem.Mol

InputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

Output

alias of schrodinger.application.steps.dataclasses.ScoredMol

OutputSerializer

alias of schrodinger.application.steps.dataclasses.ScoredMolSerializer

class schrodinger.application.steps.dataclasses.MaeInMixin

Bases: object

Input

alias of schrodinger.structure._structure.Structure

class schrodinger.application.steps.dataclasses.MaeOutMixin

Bases: object

Output

alias of schrodinger.structure._structure.Structure

class schrodinger.application.steps.dataclasses.MaeMaeMixin

Bases: schrodinger.application.steps.dataclasses.MaeInMixin, schrodinger.application.steps.dataclasses.MaeOutMixin

class schrodinger.application.steps.dataclasses.FileInMixin

Bases: object

Input

alias of schrodinger.stepper.stepper.StepperFile