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(bool suppressH=true)

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(const OEDepictionFrom3DOptions &rhs)

Copy constructor.

operator=

OEDepictionFrom3DOptions &operator=(const OEDepictionFrom3DOptions &rhs)

Assignment operator.

GetCoordsToInertialFrame

bool GetCoordsToInertialFrame() const

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

GetMaxBondRotations

unsigned int GetMaxBondRotations() const

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.

GetRotateTo2DReference

bool GetRotateTo2DReference() const

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

GetSuppressHydrogens

bool GetSuppressHydrogens() const

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

SetCoordsToInertialFrame

void SetCoordsToInertialFrame(bool)

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

SetMaxBondRotations

void SetMaxBondRotations(unsigned int maxrotations)

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.

SetRotateTo2DReference

void SetRotateTo2DReference(bool)

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.

SetSuppressHydrogens

void SetSuppressHydrogens(bool suppressH)

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.