OE2DMolDisplay

class OE2DMolDisplay : public OEMolDisplayBase

This class represents OE2DMolDisplay that stores the depiction information (such as atom coordinates, molecule scaling, representation styles etc.) of a molecule. See Figure: OEDepict TK molecule display class hierarchy.

../../_images/OEMolDisplayHierarchy.png — **OEDepict TK molecule display class hierarchy**

See also

The following methods are publicly inherited from OEMolDisplayBase:

GetDataType

GetMolecule

IsDataType

Constructors

OE2DMolDisplay(arg2: Union[OEGraphMol,OEMol,OEQMol]) -> OE2DMolDisplay

Initializes an OE2DMolDisplay object using default display options.

mol: The molecule for which display information is stored in the OE2DMolDisplay object.

See also

OE2DMolDisplayOptions.Constructors method for the list of default display options
OE2DMolDisplay.IsValid method

OE2DMolDisplay(arg2: Union[OEGraphMol,OEMol,OEQMol],
               arg3: OE2DMolDisplayOptions) -> OE2DMolDisplay

Initializes an OE2DMolDisplay object using the given display options.

mol: The molecule for which display information is stored in the OE2DMolDisplay object.
opts: The OE2DMolDisplayOptions object that stores properties that determine the styles of the molecule depiction.

Warning

An OE2DMolDisplay object does not make a copy of the OEMolBase object from which it is initialized but only stores its pointer. Therefore, the user responsibility is to not let the molecule go out of scope, before the corresponding OE2DMolDisplay object.
Changing the OEMolBase object from which OE2DMolDisplay object is initialized has no effect on the display itself after initialization. However, the OE2DMolDisplay object become invalid if the molecule graph is modified (atoms or bonds added or deleted).

Note

A warning is thrown when an OE2DMolDisplay object is initialized with a molecule with 3D coordinates.
An OE2DMolDisplay object is considered invalid and an error is thrown when it is initialized:
- with an empty molecule (i.e. molecule with no atoms)
- with a molecule that has neither 2D nor 3D coordinates
See also: OE2DMolDisplay.IsValid method

OE2DMolDisplay(rhs: OE2DMolDisplay) -> OE2DMolDisplay

Copy constructor.

CreateCopy

CreateCopy() -> OEBase

Deep copy constructor that returns a copy of the object. The memory for the returned OE2DMolDisplay object is dynamically allocated and owned by the caller.

GetAtomDisplay

GetAtomDisplay(atom: OEAtomBase) -> OE2DAtomDisplay

Returns the pointer of the OE2DAtomDisplay object that stores the depiction information of the given atom.

GetAtomDisplay(atom: OEAtomBase) -> OE2DAtomDisplay

Returns the const pointer of the OE2DAtomDisplay object that stores the depiction information of the given atom.

Note

The OE2DMolDisplay.GetAtomDisplay methods returns a zero pointer if the given atom does not correspond to any display atom stored in the OE2DMolDisplay object. It is a good programming practice to check the returned pointer before using it. See code snippet below.

adisp = disp.GetAtomDisplay(atom)
if adisp is not None and adisp.IsVisible():
    # do something
    pass

See also

OE2DAtomDisplay class

GetAtomDisplays

GetAtomDisplays() -> Iterable[OE2DAtomDisplay]

Returns an iterator over all OE2DAtomDisplay objects stored in the OE2DMolDisplay object.

GetAtomDisplays(pred: OEUnaryAtomPred) -> Iterable[OE2DAtomDisplay]

Returns an iterator over only those OE2DAtomDisplay objects for which the corresponding atom passes the given predicate. For example, the following code snippet shows how to access the atom displays of oxygen atoms:

for adisp in disp.GetAtomDisplays(oechem.OEHasAtomicNum(oechem.OEElemNo_O)):
    if adisp.IsVisible():
        # do something
        pass

See also

OE2DAtomDisplay class
Listing 4 example in the Customizing Molecule Depiction section

GetBondDisplay

GetBondDisplay(bond: OEBondBase) -> OE2DBondDisplay

Returns the pointer of the OE2DBondDisplay object, that stores the depiction information of the given bond.

GetBondDisplay(bond: OEBondBase) -> OE2DBondDisplay

Returns the const pointer of the OE2DBondDisplay object, that stores the depiction information of the given bond.

See also

OE2DBondDisplay class

Note

The OE2DMolDisplay.GetBondDisplay methods returns a zero pointer if the given bond does not correspond to any display bond stored in the OE2DMolDisplay object. It is a good programming practice to check the returned pointer before using it. See code snippet below.

bdisp = disp.GetBondDisplay(bond)
if bdisp is not None and bdisp.IsVisible():
    # do something
    pass

See also

OE2DBondDisplay class

GetBondDisplays

GetBondDisplays() -> Iterable[OE2DBondDisplay]

Returns an iterator over all OE2DBondDisplay objects stored in the OE2DMolDisplay object.

GetBondDisplays(pred: OEUnaryBondPred) -> Iterable[OE2DBondDisplay]

See also

OE2DBondDisplay class

Returns an iterator over only those OE2DBondDisplay objects for which the corresponding bond passes the given predicate. For example, the following code snippet shows how to access the bond displays of aromatic bonds:

for bdisp in disp.GetBondDisplays(oechem.OEIsAromaticBond()):
    if bdisp.IsVisible():
        # do something
        pass

See also

OE2DBondDisplay class
Listing 4 example in the Customizing Molecule Depiction section

GetDataType

GetDataType() -> void

This function is used to perform run-time type identification.

See also

OEBase.GetDataType method in the OEChem TK manual

GetHeight

GetHeight() -> float

Returns the height of the displayed molecule.

See also

Controlling the Size of Depicted Molecules section
OE2DMolDisplay.GetScale method
OE2DMolDisplay.GetWidth method

GetLayer

GetLayer(position: int, idx: int = 0) -> OEImage

Provides access to the layers of the OE2DMolDisplay object. Currently, an OE2DMolDisplay object has two layers (one OELayerPosition_Above and one OELayerPosition_Below ) that allows drawing of objects over or underneath the molecular structure, respectively.

position: This value has to be from the OELayerPosition namespace.
idx: This parameter is currently not used.

See also

OEImage class
OELayerPosition namespace

GetOptions

GetOptions() -> OE2DMolDisplayOptions

Returns the options used to initialized the OE2DMolDisplay object.

See also

OE2DMolDisplayOptions class

GetScale

GetScale() -> float

Returns the scaling factor of the displayed molecule.

See also

Controlling the Size of Depicted Molecules section
OE2DMolDisplay.GetHeight method
OE2DMolDisplay.GetWidth method

GetWidth

GetWidth() -> float

Returns the width of the displayed molecule.

See also

Controlling the Size of Depicted Molecules section
OE2DMolDisplay.GetHeight method
OE2DMolDisplay.GetScale method

IsDataType

IsDataType(arg2: void) -> bool

Returns whether type is the same as the instance this method is called on.

See also

OEBase.IsDataType method in the OEChem TK manual

IsValid

IsValid() -> bool

Returns whether the OE2DMolDisplay object was initialized successfully. If initialization was attempted with an empty molecule or a molecule with no coordinates (neither 2D nor 3D), then this method returns false. An OE2DMolDisplay object becomes invalid if the molecule, from which it was initialized, is modified. For example, atom or bonds added to or deleted from the molecule.

Hint

It is highly recommend to check whether a molecule display is valid after initialization.