#include <DrawMolMCH.h>

Inheritance diagram for RDKit::MolDraw2D_detail::DrawMolMCH:

Public Member Functions
	DrawMolMCH (const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1)

	DrawMolMCH (const DrawMol &)=delete

	DrawMolMCH (DrawMol &&)=delete

DrawMolMCH &	operator= (const DrawMol &)=delete

DrawMolMCH &	operator= (DrawMol &&)=delete

void	extractHighlights (double scale) override

virtual void	extractMCHighlights ()=0

void	getAtomRadius (unsigned int atomIdx, double &xradius, double &yradius) const

Public Member Functions inherited from RDKit::MolDraw2D_detail::DrawMol
virtual	~DrawMol ()=default

	DrawMol (const ROMol &mol, const std::string &legend, int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, const std::vector< int > highlightAtoms=nullptr, const std::vector< int > highlightBonds=nullptr, const std::map< int, DrawColour > highlightAtomMap=nullptr, const std::map< int, DrawColour > highlightBondMap=nullptr, const std::vector< std::pair< DrawColour, DrawColour > > bondColours=nullptr, const std::map< int, double > highlight_radii=nullptr, bool includeAnnotations=true, int confId=-1, bool isReactionMol=false)

	DrawMol (int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, double xmin, double xmax, double ymin, double ymax, double scale, double fontscale)

	DrawMol (const DrawMol &)=delete

	DrawMol (DrawMol &&)=delete

DrawMol &	operator= (const DrawMol &)=delete

DrawMol &	operator= (DrawMol &&)=delete

void	createDrawObjects ()

void	finishCreateDrawObjects ()

void	initDrawMolecule (const ROMol &mol)

void	extractAll (double scale)

void	extractAtomCoords ()

void	extractAtomSymbols ()

void	extractBonds ()

void	extractRegions ()

void	extractAttachments ()

void	extractMolNotes ()

void	extractCIPCodes (bool showAllCIPCodes)

void	extractStereoGroups ()

void	extractAtomNotes ()

void	extractBondNotes ()

void	extractRadicals ()

void	extractSGroupData ()

void	extractVariableBonds ()

void	extractBrackets ()

void	extractLinkNodes ()

void	extractCloseContacts ()

void	resolveAtomSymbolClashes ()

void	calculateScale ()

void	findExtremes ()

void	changeToDrawCoords ()

void	draw (MolDraw2D &drawer) const

void	drawRadicals (MolDraw2D &drawer) const

void	resetEverything ()

void	shrinkToFit (bool withPadding=true)

std::pair< std::string, OrientType >	getAtomSymbolAndOrientation (const Atom &atom) const

std::string	getAtomSymbol (const Atom &atom, OrientType orientation) const

OrientType	getAtomOrientation (const Atom &atom) const

void	partitionForLegend ()

void	extractLegend ()

void	calcMeanBondLength ()

void	makeStandardBond (Bond *bond, double doubleBondOffset)

void	makeQueryBond (Bond *bond, double doubleBondOffset)

void	makeDoubleBondLines (Bond *bond, double doubleBondOffset, const std::pair< DrawColour, DrawColour > &cols)

void	makeTripleBondLines (Bond *bond, double doubleBondOffset, const std::pair< DrawColour, DrawColour > &cols)

void	makeWedgedBond (Bond *bond, const std::pair< DrawColour, DrawColour > &cols)

void	makeWavyBond (Bond *bond, double offset, const std::pair< DrawColour, DrawColour > &cols)

void	makeDativeBond (Bond *bond, double offset, const std::pair< DrawColour, DrawColour > &cols)

void	makeZeroBond (Bond *bond, const std::pair< DrawColour, DrawColour > &cols, const DashPattern &dashPattern)

void	adjustBondEndsForLabels (int begAtIdx, int endAtIdx, Point2D &begCds, Point2D &endCds) const

void	newBondLine (const Point2D &pt1, const Point2D &pt2, const DrawColour &col1, const DrawColour &col2, int atom1Idx, int atom2Idx, int bondIdx, const DashPattern &dashPattern)

std::pair< DrawColour, DrawColour >	getBondColours (Bond *bond)

void	makeContinuousHighlights (double scale)

void	makeAtomCircleHighlights ()

void	makeAtomEllipseHighlights (double lineWidth)

void	makeBondHighlightLines (double lineWidth, double scale)

void	calcAnnotationPosition (const Atom *atom, DrawAnnotation &annot) const

void	calcAnnotationPosition (const Bond *bond, DrawAnnotation &annot) const

double	getNoteStartAngle (const Atom *atom) const

int	doesNoteClash (const DrawAnnotation &annot) const

int	doesRectClash (const StringRect &rect, double padding) const

OrientType	calcRadicalRect (const Atom *atom, StringRect &rad_rect) const

void	getDrawTransformers (Point2D &trans, Point2D &scale, Point2D &toCentre) const

Point2D	getDrawCoords (const Point2D &atCds, const Point2D &trans, const Point2D &scaleFactor, const Point2D &toCentre) const

Point2D	getDrawCoords (const Point2D &atCds) const

Point2D	getDrawCoords (int atnum) const

Point2D	getAtomCoords (const Point2D &screenCds) const

Point2D	getAtomCoords (int atnum) const

double	getScale () const

double	getFontScale () const

void	setScale (double newScale, double newFontScale, bool ignoreFontLimits=true)

void	setTransformation (const DrawMol &sourceMol)

void	setOffsets (double xOffset, double yOffset)

void	tagAtomsWithCoords ()

void	transformAll (const Point2D trans=nullptr, Point2D scale=nullptr, const Point2D *toCentre=nullptr)

Point2D	transformPoint (const Point2D &pt, const Point2D trans=nullptr, Point2D scale=nullptr, const Point2D *toCentre=nullptr) const

void	calcDoubleBondLines (double offset, const Bond &bond, Point2D &l1s, Point2D &l1f, Point2D &l2s, Point2D &l2f) const

void	bondInsideRing (const Bond &bond, double offset, Point2D &l2s, Point2D &l2f) const

void	bondNonRing (const Bond &bond, double offset, Point2D &l2s, Point2D &l2f) const

void	doubleBondTerminal (Atom at1, Atom at2, double offset, Point2D &l1s, Point2D &l1f, Point2D &l2s, Point2D &l2f) const

Point2D	doubleBondEnd (unsigned int at1, unsigned int at2, unsigned int at3, double offset, bool trunc) const

void	calcTripleBondLines (double offset, const Bond &bond, Point2D &l1s, Point2D &l1f, Point2D &l2s, Point2D &l2f)

void	findOtherBondVecs (const Atom atom, const Atom otherAtom, std::vector< Point2D > &otherBondVecs) const

void	adjustBondsOnSolidWedgeEnds ()

void	smoothBondJoins ()

void	makeHighlightEnd (const Atom end1, const Atom end2, double lineWidth, const std::vector< Atom * > &end1HighNbrs, std::vector< Point2D > &points)

DrawColour	getColour (int atom_idx) const

Public Attributes
const std::map< int, std::vector< DrawColour > > &	mcHighlightAtomMap_

const std::map< int, std::vector< DrawColour > > &	mcHighlightBondMap_

const std::map< int, int > &	highlightLinewidthMultipliers_

Public Attributes inherited from RDKit::MolDraw2D_detail::DrawMol
const MolDrawOptions &	drawOptions_

DrawText &	textDrawer_

double	marginPadding_

std::vector< int >	highlightAtoms_

std::vector< int >	highlightBonds_

std::map< int, DrawColour >	highlightAtomMap_

std::map< int, DrawColour >	highlightBondMap_

std::vector< std::pair< DrawColour, DrawColour > >	bondColours_

std::map< int, double >	highlightRadii_

bool	includeAnnotations_

bool	isReactionMol_

std::string	legend_

std::unique_ptr< RWMol >	drawMol_

int	confId_

std::vector< Point2D >	atCds_

std::vector< std::unique_ptr< DrawShape > >	bonds_

std::vector< std::unique_ptr< DrawShape > >	preShapes_

std::vector< std::unique_ptr< DrawShape > >	postShapes_

std::vector< int >	atomicNums_

std::vector< std::pair< std::string, OrientType > >	atomSyms_

std::vector< std::unique_ptr< AtomSymbol > >	atomLabels_

std::vector< std::unique_ptr< DrawShape > >	highlights_

std::vector< std::unique_ptr< DrawAnnotation > >	annotations_

std::vector< std::unique_ptr< DrawAnnotation > >	legends_

std::vector< std::tuple< StringRect, OrientType, int > >	radicals_

std::vector< int >	singleBondLines_

int	width_

int	height_

int	drawWidth_

int	drawHeight_

double	scale_

double	fontScale_

double	xMin_

double	yMin_

double	xMax_

double	yMax_

double	xRange_

double	yRange_

double	xOffset_ = 0.0

double	yOffset_ = 0.0

double	meanBondLength_ = 0.0

int	molHeight_

int	legendHeight_ = 0

bool	drawingInitialised_ = false

int	activeAtmIdxOffset_ = 0

int	activeBndIdxOffset_ = 0

bool	flexiCanvasX_ = false

bool	flexiCanvasY_ = false

Detailed Description

Definition at line 25 of file DrawMolMCH.h.

Constructor & Destructor Documentation

◆ DrawMolMCH() [1/3]

RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH	(	const ROMol &	mol,
		const std::string &	legend,
		int	width,
		int	height,
		MolDrawOptions &	drawOptions,
		DrawText &	textDrawer,
		const std::map< int, std::vector< DrawColour > > &	highlight_atom_map,
		const std::map< int, std::vector< DrawColour > > &	highlight_bond_map,
		const std::map< int, double > &	highlight_radii,
		const std::map< int, int > &	highlight_linewidth_multipliers,
		int	confId = -1 )

Make a DrawMol that does multi-coloured highlights. Both atoms and bonds can have more than 1 highlight. There's no maximum although more than 4 is very cluttered.

Parameters

mol	: the molecule to draw
legend	: the legend (to be drawn under the molecule)
width	: width (in pixels) of the rendering set this to -1 to have the canvas size set automatically
height	: height (in pixels) of the rendering set this to -1 to have the canvas size set automatically
drawOptions	: a MolDrawOptions object from the owning MolDraw2D
textDrawer	: a DrawText object from the owning MolDraw2D
highlight_atom_map	: indexed on atom idx, the colours to be used to highlight atoms. Not all atoms need to be mentioned.
highlight_bond_map	: indexed on bond idx, the colours to be used to highlight bonds. Not all bonds need to be mentioned.
highlightRadii	: map from atomId -> radius (in molecule coordinates) for the radii of atomic highlights. If not provided for an atom, the default value from `drawOptions()` will be used.
highlight_linewidth_multipliers	: map from bondId -> int, to change the thickness of the lines used for the highlighting.
confId	: (optional) conformer ID to be used for atomic coordinates