OEAlignedDepictionFrom3DOptions

class OEAlignedDepictionFrom3DOptions

This class represents OEAlignedDepictionFrom3DOptions that stores parameters that are used when generating 2D coordinates by calling the OEPrepareAlignedDepictionFrom3D function.

Property Get method Set method
clear coords GetClearCoords SetClearCoords
max number of bond rotations GetMaxBondRotations SetMaxBondRotations
suppressing hydrogens GetSuppressHydrogens SetSuppressHydrogens

Constructors

OEAlignedDepictionFrom3DOptions(bool clearCoords=true, bool suppressH=true)

Default constructor that initializes an OEAlignedDepictionFrom3DOptions object with the following properties:

Default parameters of the OEAlignedDepictionFrom3DOptions class
Property Default value
clear coordinates true
max number of bond rotations \(2^{16} = 65536\)
suppressing hydrogens true
OEAlignedDepictionFrom3DOptions(const OEAlignedDepictionFrom3DOptions &rhs)

Copy constructor.

operator=

OEAlignedDepictionFrom3DOptions &
  operator=(const OEAlignedDepictionFrom3DOptions &rhs)

Assignment operator.

GetClearCoords

bool GetClearCoords() const

GetMaxBondRotations

unsigned int GetMaxBondRotations() const

GetSuppressHydrogens

bool GetSuppressHydrogens() const

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

SetClearCoords

void SetClearCoords(bool clearcoords)

If false and the fit molecule has 2D coordinates, then these coordinates are used for the alignment. Otherwise the 2D coordinates of the fitted molecule are generated by calling the OEPrepareDepictionFrom3D function.

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 “best” aligned 2D coordinates.

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 “best” aligned 2D layout.

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

SetSuppressHydrogens

void SetSuppressHydrogens(bool)

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.