OEPrepareDepictionOptions

class OEPrepareDepictionOptions

This class represents OEPrepareDepictionOptions that stores the following parameters that are used when preparing a molecule for depiction.

Property	Get method	Set method	Corresponding namespace / type
re-generating 2D coordinates	GetClearCoords	SetClearCoords	boolean
adding depiction hydrogens	GetAddDepictionHydrogens	SetAddDepictionHydrogens	boolean
perceiving MDL bond stereo (wedge/hash)	GetPerceiveBondStereo	SetPerceiveBondStereo	boolean
suppressing explicit (non-depiction) hydrogens	GetSuppressHydrogens	SetSuppressHydrogens	boolean
depiction orientation	GetDepictOrientation	SetDepictOrientation	OEDepictOrientation

See also

• OEPrepareDepiction function

See the effect of the above parameters in Table: Depictions generated with various parameter combinations when depiction are generated from the following input:

SMILES

Parsing the “CC([C@@H]1C[C@@H]2C[C@H]1NC2)N(H)(H)” string with three explicit hydrogens necessary to define tetrahedral stereo centers and two additional explicit hydrogens.

MDL

Reading an MDL file with 2D coordinates and pre-assigned wedge/hash bonds. It also includes two explicit hydrogens.

Depictions generated with various parameter combinations

index	clear coordinates	suppress explicit H	add depict H	perceive wedge/hash	from SMILES	from MDL
(1)	F	F	F	F
(2)	F	F	F	T
(3)	F	F	T	F
(4)	F	F	T	T
(5)	F	T	F	F
(6)	F	T	F	T
(7)	F	T	T	F
(8)	F	T	T	T
(9)	T	F	F	F
(10)	T	F	F	T
(11)	T	F	T	F
(12)	T	F	T	T
(13)	T	T	F	F
(14)	T	T	F	T
(15)	T	T	T	F
(16)	T	T	T	T

Comments:

(1)

MDL = no op; SMILES = generating 2D coordinates is necessary

(4)

MDL = keeping original 2D coordinates, adding depiction hydrogens, re-perceiving wedge/hash bonds; SMILES = generating 2D coordinates, depiction hydrogens are kept; perceiving wedge/hash bonds

(8)

Default parameters; MDL = keeping original 2D coordinates, re-perceiving all other information; SMILES = generating 2D coordinates, regenerating all other information;

(10)

MDL = regenerating 2D coordinates and re-perceiving wedge/hash bonds (since no depiction hydrogens are added the wedge/hash bonds are on ring bonds); SMILES generating 2D coordinates and perceiving wedge/hash bonds;

(12)

Regenerating all information and keeping all explicit hydrogens

(16)

Regenerating all information; the depiction of identical molecules imported from SMILES and MDL will be identical

Constructors

OEPrepareDepictionOptions(bool clearcoords=false, bool suppressH=true)

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

clearcoords

See the OEPrepareDepictionOptions.SetClearCoords method.

suppressH

See the OEPrepareDepictionOptions.SetSuppressHydrogens method.

Default parameters of the OEPrepareDepictionOptions class

Property	Default value
re-generating 2D coordinates	false
adding depiction hydrogens	true
perceiving MDL bond stereo (wedge/hash)	true
suppressing explicit (non-depiction) hydrogens	true
depiction orientation	OEDepictOrientation.Default

OEPrepareDepictionOptions(const OEPrepareDepictionOptions &rhs)

Copy constructor.

operator=

OEPrepareDepictionOptions &operator=(const OEPrepareDepictionOptions &rhs)

Assignment operator.

GetAddDepictionHydrogens

bool GetAddDepictionHydrogens() const

Returns whether the depiction hydrogens are kept/added.

See also

• OEPrepareDepictionOptions.SetAddDepictionHydrogens method

GetClearCoords

bool GetClearCoords() const

Returns whether the 2D coordinates of a molecule are re-calculated.

See also

• OEPrepareDepictionOptions.SetClearCoords method

GetDepictOrientation

unsigned int GetDepictOrientation() const

Returns the preferred orientation of the 2D coordinates. The return value is taken from the OEDepictOrientation namespace.

See also

• OEPrepareDepictionOptions.SetDepictOrientation method

GetPerceiveBondStereo

bool GetPerceiveBondStereo() const

Returns whether the hash/wedge bonds are re-assigned.

See also

• OEPrepareDepictionOptions.SetPerceiveBondStereo method

GetSuppressHydrogens

bool GetSuppressHydrogens() const

Returns whether the explicit (non-depiction) hydrogens are suppressed.

See also

• OEPrepareDepictionOptions.SetSuppressHydrogens method

SetAddDepictionHydrogens

void SetAddDepictionHydrogens(bool)

Sets whether depiction hydrogens are kept/added.

See also

• OEAddDepictionHydrogens function

• OEPrepareDepictionOptions.GetAddDepictionHydrogens method

SetClearCoords

void SetClearCoords(bool clearcoords)

Sets whether the 2D coordinates of the molecule are re-calculated. If the molecule has no 2D coordinates, then the 2D coordinates are always calculated by calling the OEDepictCoordinates regardless of this setting.

See also

• OEDepictCoordinates function

• OEPrepareDepictionOptions.GetClearCoords method

SetDepictOrientation

void SetDepictOrientation(unsigned int orientation)

Sets the preferred orientation of the 2D coordinates.

orientation

This value has to be from the OEDepictOrientation namespace.

See also

• OEPrepareDepictionOptions.GetDepictOrientation method

• OEDepictOrientation namespace

SetPerceiveBondStereo

void SetPerceiveBondStereo(bool)

Sets whether to re-assign the wedge and hash bonds by calling the OEMDLPerceiveBondStereo function.

See also

• OEMDLPerceiveBondStereo function in the OEChem TK manual

• OEPrepareDepictionOptions.GetPerceiveBondStereo method

SetSuppressHydrogens

void SetSuppressHydrogens(bool)

Sets whether the explicit (non-depiction) hydrogens are suppressed in the molecule. Only hydrogens that are necessary to faithfully represent tetrahedral stereo-chemistry will be kept.

See also

• OESuppressHydrogens function in the OEChem TK manual

• OEPrepareDepictionOptions.GetSuppressHydrogens method