RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine Class Reference

#include <DrawMolMCHCircleAndLine.h>

Inheritance diagram for RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine:

Public Member Functions
	DrawMolMCHCircleAndLine (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)
	DrawMolMCHCircleAndLine (const DrawMol &)=delete
	DrawMolMCHCircleAndLine (DrawMol &&)=delete
DrawMolMCHCircleAndLine &	operator= (const DrawMol &)=delete
DrawMolMCHCircleAndLine &	operator= (DrawMol &&)=delete
void	extractHighlights (double scale) override
void	extractMCHighlights () override
void	makeBondHighlights (std::vector< std::unique_ptr< DrawShape > > &bondHighlights)
void	makeAtomHighlights (std::vector< std::unique_ptr< DrawShape > > &atomHighlights)
void	adjustLineEndForHighlight (int at_idx, Point2D p1, Point2D &p2) const
void	calcSymbolEllipse (unsigned int atomIdx, Point2D &centre, double &xradius, double &yradius) const
void	fixHighlightJoinProblems (std::vector< std::unique_ptr< DrawShape > > &atomHighlights, std::vector< std::unique_ptr< DrawShape > > &bondHighlights)
Public Member Functions inherited from 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)
	DrawMolMCH (const DrawMol &)=delete
	DrawMolMCH (DrawMol &&)=delete
DrawMolMCH &	operator= (const DrawMol &)=delete
DrawMolMCH &	operator= (DrawMol &&)=delete
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

Additional Inherited Members
Public Attributes inherited from RDKit::MolDraw2D_detail::DrawMolMCH
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 21 of file DrawMolMCHCircleAndLine.h.

Constructor & Destructor Documentation

DrawMolMCHCircleAndLine() [1/3]

RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::DrawMolMCHCircleAndLine	(	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

Referenced by operator=(), and operator=().

DrawMolMCHCircleAndLine() [2/3]

RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::DrawMolMCHCircleAndLine ( const DrawMol & )

delete

DrawMolMCHCircleAndLine() [3/3]

RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::DrawMolMCHCircleAndLine ( DrawMol && )

delete

Member Function Documentation

adjustLineEndForHighlight()

void RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::adjustLineEndForHighlight	(	int	at_idx,
		Point2D	p1,
		Point2D &	p2 ) const

calcSymbolEllipse()

void RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse	(	unsigned int	atomIdx,
		Point2D &	centre,
		double &	xradius,
		double &	yradius ) const

extractHighlights()

void RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractHighlights ( double scale )

overridevirtual

Reimplemented from RDKit::MolDraw2D_detail::DrawMolMCH.

extractMCHighlights()

void RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights ( )

overridevirtual

Implements RDKit::MolDraw2D_detail::DrawMolMCH.

fixHighlightJoinProblems()

void RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::fixHighlightJoinProblems	(	std::vector< std::unique_ptr< DrawShape > > &	atomHighlights,
		std::vector< std::unique_ptr< DrawShape > > &	bondHighlights )

makeAtomHighlights()

void RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights

(

std::vector< std::unique_ptr< DrawShape > > &

atomHighlights

)

makeBondHighlights()

void RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights

(

std::vector< std::unique_ptr< DrawShape > > &

bondHighlights

)

operator=() [1/2]

DrawMolMCHCircleAndLine & RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::operator= ( const DrawMol & )

delete

References DrawMolMCHCircleAndLine().

operator=() [2/2]

DrawMolMCHCircleAndLine & RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::operator= ( DrawMol && )

delete

References DrawMolMCHCircleAndLine().

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The documentation for this class was generated from the following file:

• DrawMolMCHCircleAndLine.h