RDKit::MolDraw2DUtils Namespace Reference

Classes
struct	ContourParams

Functions
RDKIT_MOLDRAW2D_EXPORT void	prepareMolForDrawing (RWMol &mol, bool kekulize=true, bool addChiralHs=true, bool wedgeBonds=true, bool forceCoords=false, bool wavyBonds=false)
	Does some cleanup operations on the molecule to prepare it to draw nicely.
RDKIT_MOLDRAW2D_EXPORT void	prepareAndDrawMolecule (MolDraw2D &drawer, const ROMol &mol, const std::string &legend="", const std::vector< int > *highlight_atoms=nullptr, const std::vector< int > *highlight_bonds=nullptr, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1, bool kekulize=true, bool addChiralHs=true, bool wedgeBonds=true, bool forceCoords=false, bool wavyBonds=false)
	prepare a molecule for drawing and draw it
RDKIT_MOLDRAW2D_EXPORT void	updateDrawerParamsFromJSON (MolDraw2D &drawer, const char *json)
RDKIT_MOLDRAW2D_EXPORT void	updateDrawerParamsFromJSON (MolDraw2D &drawer, const std::string &json)
RDKIT_MOLDRAW2D_EXPORT void	updateMolDrawOptionsFromJSON (MolDrawOptions &opts, const char *json)
RDKIT_MOLDRAW2D_EXPORT void	updateMolDrawOptionsFromJSON (MolDrawOptions &opts, const std::string &json)
RDKIT_MOLDRAW2D_EXPORT void	contourAndDrawGrid (MolDraw2D &drawer, const double *grid, const std::vector< double > &xcoords, const std::vector< double > &ycoords, size_t nContours, std::vector< double > &levels, const ContourParams &ps=ContourParams(), const ROMol *mol=nullptr)
	Generates and draws contours for data on a grid.
RDKIT_MOLDRAW2D_EXPORT void	contourAndDrawGrid (MolDraw2D &drawer, const double *grid, const std::vector< double > &xcoords, const std::vector< double > &ycoords, size_t nContours=10, const ContourParams &ps=ContourParams(), const ROMol *mol=nullptr)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_MOLDRAW2D_EXPORT void	contourAndDrawGaussians (MolDraw2D &drawer, const std::vector< Point2D > &locs, const std::vector< double > &heights, const std::vector< double > &widths, size_t nContours, std::vector< double > &levels, const ContourParams &ps=ContourParams(), const ROMol *mol=nullptr)
	Generates and draws contours for a set of gaussians.
RDKIT_MOLDRAW2D_EXPORT void	contourAndDrawGaussians (MolDraw2D &drawer, const std::vector< Point2D > &locs, const std::vector< double > &heights, const std::vector< double > &widths, size_t nContours=10, const ContourParams &ps=ContourParams(), const ROMol *mol=nullptr)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_MOLDRAW2D_EXPORT void	drawMolACS1996 (MolDraw2D &drawer, const ROMol &mol, const std::string &legend, const std::vector< int > *highlight_atoms, const std::vector< int > *highlight_bonds, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1)
	Draw a molecule to a MolDraw2D object according to ACS 1996 guidelines.
RDKIT_MOLDRAW2D_EXPORT void	setACS1996Options (MolDrawOptions &opts, double meanBondLen=1.0)
RDKIT_MOLDRAW2D_EXPORT double	meanBondLength (const ROMol &mol, int confId=-1)

Function Documentation

contourAndDrawGaussians() [1/2]

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::contourAndDrawGaussians	(	MolDraw2D &	drawer,
		const std::vector< Point2D > &	locs,
		const std::vector< double > &	heights,
		const std::vector< double > &	widths,
		size_t	nContours,
		std::vector< double > &	levels,
		const ContourParams &	ps = ContourParams(),
		const ROMol *	mol = nullptr
	)

Generates and draws contours for a set of gaussians.

Referenced by contourAndDrawGaussians().

contourAndDrawGaussians() [2/2]

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::contourAndDrawGaussians ( MolDraw2D &  drawer, const std::vector< Point2D > &  locs, const std::vector< double > &  heights, const std::vector< double > &  widths, size_t  nContours = 10, const ContourParams &  ps = ContourParams(), const ROMol *  mol = nullptr  )

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 179 of file MolDraw2DUtils.h.

References contourAndDrawGaussians(), and RDKit::rdvalue_is().

contourAndDrawGrid() [1/2]

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::contourAndDrawGrid	(	MolDraw2D &	drawer,
		const double *	grid,
		const std::vector< double > &	xcoords,
		const std::vector< double > &	ycoords,
		size_t	nContours,
		std::vector< double > &	levels,
		const ContourParams &	ps = ContourParams(),
		const ROMol *	mol = nullptr
	)

Generates and draws contours for data on a grid.

Referenced by contourAndDrawGrid().

contourAndDrawGrid() [2/2]

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::contourAndDrawGrid ( MolDraw2D &  drawer, const double *  grid, const std::vector< double > &  xcoords, const std::vector< double > &  ycoords, size_t  nContours = 10, const ContourParams &  ps = ContourParams(), const ROMol *  mol = nullptr  )

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 136 of file MolDraw2DUtils.h.

References contourAndDrawGrid(), and RDKit::rdvalue_is().

drawMolACS1996()

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::drawMolACS1996	(	MolDraw2D &	drawer,
		const ROMol &	mol,
		const std::string &	legend,
		const std::vector< int > *	highlight_atoms,
		const std::vector< int > *	highlight_bonds,
		const std::map< int, DrawColour > *	highlight_atom_map = nullptr,
		const std::map< int, DrawColour > *	highlight_bond_map = nullptr,
		const std::map< int, double > *	highlight_radii = nullptr,
		int	confId = -1
	)

Draw a molecule to a MolDraw2D object according to ACS 1996 guidelines.

meanBondLength()

RDKIT_MOLDRAW2D_EXPORT double RDKit::MolDraw2DUtils::meanBondLength	(	const ROMol &	mol,
		int	confId = -1
	)

prepareAndDrawMolecule()

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::prepareAndDrawMolecule	(	MolDraw2D &	drawer,
		const ROMol &	mol,
		const std::string &	legend = "",
		const std::vector< int > *	highlight_atoms = nullptr,
		const std::vector< int > *	highlight_bonds = nullptr,
		const std::map< int, DrawColour > *	highlight_atom_map = nullptr,
		const std::map< int, DrawColour > *	highlight_bond_map = nullptr,
		const std::map< int, double > *	highlight_radii = nullptr,
		int	confId = -1,
		bool	kekulize = true,
		bool	addChiralHs = true,
		bool	wedgeBonds = true,
		bool	forceCoords = false,
		bool	wavyBonds = false
	)

prepare a molecule for drawing and draw it

prepareMolForDrawing()

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::prepareMolForDrawing	(	RWMol &	mol,
		bool	kekulize = true,
		bool	addChiralHs = true,
		bool	wedgeBonds = true,
		bool	forceCoords = false,
		bool	wavyBonds = false
	)

Does some cleanup operations on the molecule to prepare it to draw nicely.

setACS1996Options()

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::setACS1996Options	(	MolDrawOptions &	opts,
		double	meanBondLen = 1.0
	)

Set the draw options to produce something as close as possible to the ACS 1996 guidelines as described at https://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style/Chemistry/Structure_drawing

updateDrawerParamsFromJSON() [1/2]

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::updateDrawerParamsFromJSON	(	MolDraw2D &	drawer,
		const char *	json
	)

updateDrawerParamsFromJSON() [2/2]

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::updateDrawerParamsFromJSON	(	MolDraw2D &	drawer,
		const std::string &	json
	)

updateMolDrawOptionsFromJSON() [1/2]

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::updateMolDrawOptionsFromJSON	(	MolDrawOptions &	opts,
		const char *	json
	)

updateMolDrawOptionsFromJSON() [2/2]

RDKIT_MOLDRAW2D_EXPORT void RDKit::MolDraw2DUtils::updateMolDrawOptionsFromJSON	(	MolDrawOptions &	opts,
		const std::string &	json
	)