OEPosit

class OEPosit

OEPosit is used to pose predict multiconformer molecules in an active site.

The OEPosit class defines the following public methods:
Deprecated methods of the class:

Constructor

OEPosit(options: OEPositOptions = OEPositOptions()) -> OEPosit
OEPosit(arg2: OEPosit) -> OEPosit

Default and copy constructors.

Assignment operator.

AddReceptor

AddReceptor(du: OEDesignUnit) -> bool
AddReceptor(receptor: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Adds a receptor to the list of receptors to pose against. The function returns true if receptor is addded successful. The first overload expects a design unit that contains a receptor. The second overload works on a variation of molecule that contains receptor data.

Note

Since OEPosit can generate pose using any of the methods described in OEPositMethod, constraints present in the receptor may or may not play any role for the specific pose generation. Constraints only effect the generated pose when OEPositMethod_FRED or OEPositMethod_HYBRID is the underlying method.

ClearReceptors

ClearReceptors() -> None

Removes all existing receptors. Removing receptors will un-initialize an already initialized OEPosit instance.

Dock

Dock(res: OESinglePoseResult, mol: OEMol) -> int
Dock(res: OEPositResults, mol: OEMol, numPoses: int = 1) -> int

Dock the input molecule mol. The second overload can return alternate docked poses, in addition to the top scoring pose, with numPoses being the maximum desired number of poses.

The return value of this method describes the result of the docking, with a value from the OEDockingReturnCode namespace. A result of OEDockingReturnCode_Success indicates docking was successful.

GetHighScoresAreBetter

GetHighScoresAreBetter() -> bool

This always returns true for OEPosit.

GetName

GetName() -> str

Returns the name of the scoring function docked poses are scored with.

GetInvalidScore

GetInvalidScore() -> float

Returns the invalid score returned by OEPosit. These values are set up to sort invalid values in reverse order from the best reported values.

IsInitialized

IsInitialized() -> bool

Returns true if this object has been successfully initialized and is ready to dock molecules.

MethodChoice

MethodChoice(recIdx: int, mol: OEMol) -> int

Returns the method that would be used for pose prediction for a given ligand against a given receptor.

RankDesignUnits

RankDesignUnits(mol: OEMol) -> Iterable[OEDesignUnit]

Rank the design units, from best to worst receptors, to pose against, for the specified ligand.

DockMultiConformerMolecule

Warning

This is a deprecated API. Please use Dock instead.

Both overloads of this method dock inputMol into the receptor added by the OEPosit.Initialize method.

The return value of this method describes the result of the docking, with a value from the OEDockingReturnCode namespace. A result of OEDockingReturnCode_Success indicates docking was successful.

DockMultiConformerMolecule(dockedMol: Union[OEGraphMol,OEMol,OEQMol],
                           inputMol: OEMol) -> int

This overload of OEPosit.DockMultiConformerMolecule returns the top scoring pose.

dockedMol

Docked pose with the best pose prediction probability of inputMol.

inputMol

A multiconformer representation of a molecule to dock.

The score of the docked pose can be obtained by calling the GetEnergy method of dockedMol.

Initialize

Warning

This is a deprecated API. Please use AddReceptor instead.

Initialize(receptor: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Initializes OEPosit with receptor to pose ligand against. Calling initialize will remove any existing receptors in the current OEPosit instance. Function returns true if setup was successful and false otherwise.

RankReceptors

Warning

This is a deprecated API. Please use RankDesignUnits instead.

RankReceptors(mol: OEMol) -> Iterable[Union[OEGraphMol, OEMol, OEQMol]]

Rank the receptors, from best to worst, to pose against, for the specified ligand.

ScoreLigand

Warning

This is a deprecated API. This method is only compatible with DockMultiConformerMolecule, for obtaining a score (pose probability) after the pose has been generated.

Method provides invalid score when called on poses generated using Dock. The scores (pose probability) from that calculation are available in the resulting OESinglePoseResult.

ScoreLigand(pose: Union[OEGraphMol,OEMol,OEQMol]) -> float

Rescores a pose within the active site.

If an error occurs this function will return the limiting large double in C++.