OEDepictionFrom3DOptions

class OEDepictionFrom3DOptions

This class represents OEDepictionFrom3DOptions that stores parameters that are used when generating 2D coordinates by calling the OEPrepareDepictionFrom3D function.

Property	Get method	Set method
inertial frame	`GetCoordsToInertialFrame`	`SetCoordsToInertialFrame`
max number of bond rotations	`GetMaxBondRotations`	`SetMaxBondRotations`
rotate to 2D reference	`GetRotateTo2DReference`	`SetRotateTo2DReference`
suppressing hydrogens	`GetSuppressHydrogens`	`SetSuppressHydrogens`

Constructors

OEDepictionFrom3DOptions(suppressH: bool = True) -> OEDepictionFrom3DOptions

Default constructor that initializes an OEDepictionFrom3DOptions object with the following properties:

**Default parameters of the OEDepictionFrom3DOptions class**
Property	Default value
inertial frame	false
max number of bond rotations	\(2^{16} = 65536\)
rotate to 2D reference	false
suppressing hydrogens	true

OEDepictionFrom3DOptions(rhs: OEDepictionFrom3DOptions) -> OEDepictionFrom3DOptions

Copy constructor.

GetCoordsToInertialFrame

GetCoordsToInertialFrame() -> bool

Returns whether the 3D molecule is moved to its inertial frame before generating the 2D coordinates.

See also

OEDepictionFrom3DOptions.SetCoordsToInertialFrame method

GetMaxBondRotations

GetMaxBondRotations() -> int

Returns the maximum number of bond rotations performed during the 2D coordinate generation process.

The default value for maximum number of bond rotations is \(2^{16} = 65536\). This means that by default only the first 16 single bonds of the molecule will be rotated to find the ‘closest’ 2D layout to the original 3D conformation.

See also

OEDepictionFrom3DOptions.SetMaxBondRotations method

GetRotateTo2DReference

GetRotateTo2DReference() -> bool

Returns whether after the 2D coordinate generation a final rotation is performed to orient the 2D coordinates according to the 3D conformation.

See also

OEDepictionFrom3DOptions.SetRotateTo2DReference method

GetSuppressHydrogens

GetSuppressHydrogens() -> bool

Returns whether the explicit hydrogens are suppressed in the molecule prior to generating the 2D coordinates.

See also

OEDepictionFrom3DOptions.SetSuppressHydrogens method

SetCoordsToInertialFrame

SetCoordsToInertialFrame(arg2: bool) -> None

Sets whether the 3D molecule is moved to its inertial frame before generating the 2D coordinates.

See also

OEDepictionFrom3DOptions.SetCoordsToInertialFrame method

SetMaxBondRotations

SetMaxBondRotations(arg2: int) -> None

Sets the maximum number of bond rotations performed during the 2D coordinate generation process.

maxrotations

The zero value means that there is no limit. Upon reaching this limit, the process terminates and returns the 2D coordinates that is the “closest” to the original 3D coordinates up to that point.

Hint

The default value for maximum number of bond rotations is \(2^{16} = 65536\). This means that by default only the first 16 single bonds of the molecule will be rotated to find the 2D layout that is the ‘closest’ to the original 3D conformation.

It is recommended to use this parameter if the input 3D molecule has a large number of rotatable bonds.

See also

OEDepictionFrom3DOptions.GetMaxBondRotations method

SetRotateTo2DReference

SetRotateTo2DReference(arg2: bool) -> None

Sets whether after the 2D coordinate generation a final rotation is performed to orient the 2D coordinates according to the 3D conformation. This can be used to ensure that 2D molecules are oriented similarly when they 3D conformations were similar.

See also

OEDepictionFrom3DOptions.GetRotateTo2DReference method

SetSuppressHydrogens

SetSuppressHydrogens(arg2: bool) -> None

Sets whether the explicit hydrogens are suppressed in the molecule prior to generating the 2D coordinates. Only hydrogens that are necessary to faithfully represent tetrahedral stereochemistry will be kept.

See also

OEDepictionFrom3DOptions.GetSuppressHydrogens method