RDKit
Open-source cheminformatics and machine learning.
RDKit::MolDraw2DSVG Class Reference

#include <MolDraw2DSVG.h>

Inheritance diagram for RDKit::MolDraw2DSVG:
RDKit::MolDraw2D

Public Member Functions

 MolDraw2DSVG (int width, int height, std::ostream &os, int panelWidth=-1, int panelHeight=-1, bool noFreetype=false)
 
 MolDraw2DSVG (int width, int height, int panelWidth=-1, int panelHeight=-1, bool noFreetype=false)
 
void setColour (const DrawColour &col) override
 sets the current draw color More...
 
void finishDrawing ()
 
void drawLine (const Point2D &cds1, const Point2D &cds2) override
 
void drawPolygon (const std::vector< Point2D > &cds) override
 
void drawEllipse (const Point2D &cds1, const Point2D &cds2) override
 draw an ellipse More...
 
void clearDrawing () override
 clears the contents of the drawing More...
 
void drawWavyLine (const Point2D &cds1, const Point2D &cds2, const DrawColour &col1, const DrawColour &col2, unsigned int nSegments=16, double vertOffset=0.05) override
 draw a wavy line like that used to indicate unknown stereochemistry More...
 
std::string getDrawingText () const
 
void tagAtoms (const ROMol &mol) override
 
void tagAtoms (const ROMol &mol, double radius, const std::map< std::string, std::string > &events={})
 
void addMoleculeMetadata (const ROMol &mol, int confId=-1) const
 
void addMoleculeMetadata (const std::vector< ROMol * > &mols, const std::vector< int > confIds={}) const
 
void drawAnnotation (const AnnotationType &annot) override
 
virtual void tagAtoms (const ROMol &mol)
 
- Public Member Functions inherited from RDKit::MolDraw2D
 MolDraw2D (int width, int height, int panelWidth, int panelHeight)
 constructor for a particular size More...
 
virtual ~MolDraw2D ()
 
virtual Point2D getDrawCoords (const Point2D &mol_cds) const
 
virtual Point2D getDrawCoords (int at_num) const
 returns the drawing coordinates of a particular atom More...
 
virtual Point2D getAtomCoords (const std::pair< int, int > &screen_cds) const
 
virtual Point2D getAtomCoords (const std::pair< double, double > &screen_cds) const
 
virtual Point2D getAtomCoords (int at_num) const
 returns the molecular coordinates of a particular atom More...
 
virtual int width () const
 return the width of the drawing area. More...
 
virtual int height () const
 return the height of the drawing area. More...
 
virtual int panelWidth () const
 return the width of the drawing panels. More...
 
virtual int panelHeight () const
 return the height of the drawing panels. More...
 
virtual int drawHeight () const
 
double scale () const
 
void calculateScale (int width, int height, const ROMol &mol, const std::vector< int > *highlight_atoms=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1)
 
void calculateScale (int width, int height, const std::vector< ROMol * > &mols, const std::vector< std::vector< int >> *highlight_atoms, const std::vector< std::map< int, double >> *highlight_radii, const std::vector< int > *confIds, std::vector< std::unique_ptr< RWMol >> &tmols)
 
void centrePicture (int width, int height)
 
void setScale (int width, int height, const Point2D &minv, const Point2D &maxv, const ROMol *mol=nullptr)
 explicitly sets the scaling factors for the drawing More...
 
void setOffset (int x, int y)
 sets the drawing offset (in drawing coords) More...
 
Point2D offset () const
 returns the drawing offset (in drawing coords) More...
 
Point2D minPt () const
 returns the minimum point of the drawing (in molecular coords) More...
 
Point2D range () const
 returns the width and height of the grid (in molecular coords) More...
 
virtual double fontSize () const
 font size in drawing coordinate units. That's probably pixels. More...
 
virtual void setFontSize (double new_size)
 
virtual DrawColour colour () const
 returns the current draw color More...
 
virtual void setDash (const DashPattern &patt)
 sets the current dash pattern More...
 
virtual const DashPatterndash () const
 returns the current dash pattern More...
 
virtual void setLineWidth (int width)
 sets the current line width More...
 
virtual int lineWidth () const
 returns the current line width More...
 
virtual void getStringSize (const std::string &label, double &label_width, double &label_height) const
 
void getLabelSize (const std::string &label, OrientType orient, double &label_width, double &label_height) const
 
void getStringExtremes (const std::string &label, OrientType orient, const Point2D &cds, double &x_min, double &y_min, double &x_max, double &y_max) const
 
virtual void drawString (const std::string &str, const Point2D &cds)
 drawString centres the string on cds. More...
 
virtual void drawString (const std::string &str, const Point2D &cds, TextAlignType align)
 
virtual void drawTriangle (const Point2D &cds1, const Point2D &cds2, const Point2D &cds3)
 draw a triangle More...
 
virtual void drawArc (const Point2D &centre, double radius, double ang1, double ang2)
 
virtual void drawArc (const Point2D &centre, double xradius, double yradius, double ang1, double ang2)
 
virtual void drawRect (const Point2D &cds1, const Point2D &cds2)
 draw a rectangle More...
 
virtual void drawAttachmentLine (const Point2D &cds1, const Point2D &cds2, const DrawColour &col, double len=1.0, unsigned int nSegments=16)
 
virtual void drawLine (const Point2D &cds1, const Point2D &cds2, const DrawColour &col1, const DrawColour &col2)
 draw a line where the ends are different colours More...
 
virtual bool fillPolys () const
 set whether or not polygons are being filled More...
 
virtual void setFillPolys (bool val)
 returns either or not polygons should be filled More...
 
MolDrawOptionsdrawOptions ()
 returns our current drawing options More...
 
const MolDrawOptionsdrawOptions () const
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
const std::vector< Point2D > & atomCoords () const
 
const std::vector< std::pair< std::string, OrientType > > & atomSyms () const
 returns the atomic symbols of the current molecule More...
 
virtual void drawArrow (const Point2D &cds1, const Point2D &cds2, bool asPolygon=false, double frac=0.05, double angle=M_PI/6)
 Draw an arrow with either lines or a filled head (when asPolygon is true) More...
 
void tabulaRasa ()
 
virtual bool supportsAnnotations ()
 
bool hasActiveAtmIdx ()
 
int getActiveAtmIdx1 ()
 
int getActiveAtmIdx2 ()
 
void setActiveAtmIdx (int at_idx1=-1, int at_idx2=-1)
 
virtual void drawMolecule (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 single molecule More...
 
virtual void drawMolecule (const ROMol &mol, const std::vector< int > *highlight_atoms=nullptr, const std::map< int, DrawColour > *highlight_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1)
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
virtual void drawMolecule (const ROMol &mol, const std::string &legend, const std::vector< int > *highlight_atoms=nullptr, const std::map< int, DrawColour > *highlight_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1)
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
virtual void drawMolecule (const ROMol &mol, 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)
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
 
virtual void drawMoleculeWithHighlights (const ROMol &mol, const std::string &legend, 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)
 draw molecule with multiple colours allowed per atom. More...
 
virtual void drawMolecules (const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int >> *highlight_atoms=nullptr, const std::vector< std::vector< int >> *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour >> *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour >> *highlight_bond_maps=nullptr, const std::vector< std::map< int, double >> *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr)
 draw multiple molecules in a grid More...
 
virtual void drawReaction (const ChemicalReaction &rxn, bool highlightByReactant=false, const std::vector< DrawColour > *highlightColorsReactants=nullptr, const std::vector< int > *confIds=nullptr)
 draw a ChemicalReaction More...
 

Protected Member Functions

void drawBond (const ROMol &mol, const Bond *bond, int at1_idx, int at2_idx, const std::vector< int > *highlight_atoms=nullptr, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::vector< int > *highlight_bonds=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::vector< std::pair< DrawColour, DrawColour >> *bond_colours=nullptr) override
 
void drawAtomLabel (int atom_num, const DrawColour &draw_colour) override
 
void drawAnnotation (const std::string &note, const StringRect &note_rect) override
 DEPRECATED. More...
 
virtual void outputClasses ()
 
- Protected Member Functions inherited from RDKit::MolDraw2D
virtual void doContinuousHighlighting (const ROMol &mol, const std::vector< int > *highlight_atoms, const std::vector< int > *highlight_bonds, const std::map< int, DrawColour > *highlight_atom_map, const std::map< int, DrawColour > *highlight_bond_map, const std::map< int, double > *highlight_radii)
 
virtual void highlightCloseContacts ()
 
virtual double getDrawLineWidth () const
 
void get2DCoordsForReaction (ChemicalReaction &rxn, Point2D &arrowBegin, Point2D &arrowEnd, std::vector< double > &plusLocs, double spacing, const std::vector< int > *confIds)
 
void get2DCoordsMol (RWMol &mol, double &offset, double spacing, double &maxY, double &minY, int confId, bool shiftAgents, double coordScale)
 

Additional Inherited Members

- Protected Attributes inherited from RDKit::MolDraw2D
std::unique_ptr< DrawTexttext_drawer_
 
std::vector< std::pair< std::string, std::string > > d_metadata
 
unsigned int d_numMetadataEntries = 0
 

Detailed Description

Definition at line 28 of file MolDraw2DSVG.h.

Constructor & Destructor Documentation

◆ MolDraw2DSVG() [1/2]

RDKit::MolDraw2DSVG::MolDraw2DSVG ( int  width,
int  height,
std::ostream &  os,
int  panelWidth = -1,
int  panelHeight = -1,
bool  noFreetype = false 
)
inline

Definition at line 31 of file MolDraw2DSVG.h.

◆ MolDraw2DSVG() [2/2]

RDKit::MolDraw2DSVG::MolDraw2DSVG ( int  width,
int  height,
int  panelWidth = -1,
int  panelHeight = -1,
bool  noFreetype = false 
)
inline

Definition at line 39 of file MolDraw2DSVG.h.

Member Function Documentation

◆ addMoleculeMetadata() [1/2]

void RDKit::MolDraw2DSVG::addMoleculeMetadata ( const ROMol mol,
int  confId = -1 
) const

◆ addMoleculeMetadata() [2/2]

void RDKit::MolDraw2DSVG::addMoleculeMetadata ( const std::vector< ROMol * > &  mols,
const std::vector< int >  confIds = {} 
) const

◆ clearDrawing()

void RDKit::MolDraw2DSVG::clearDrawing ( )
overridevirtual

clears the contents of the drawing

Implements RDKit::MolDraw2D.

◆ drawAnnotation() [1/2]

void RDKit::MolDraw2DSVG::drawAnnotation ( const AnnotationType annot)
overridevirtual

Reimplemented from RDKit::MolDraw2D.

◆ drawAnnotation() [2/2]

void RDKit::MolDraw2DSVG::drawAnnotation ( const std::string &  note,
const StringRect note_rect 
)
inlineoverrideprotectedvirtual

DEPRECATED.

Reimplemented from RDKit::MolDraw2D.

Definition at line 99 of file MolDraw2DSVG.h.

References RDKit::AnnotationType::rect_, and RDKit::AnnotationType::text_.

◆ drawAtomLabel()

void RDKit::MolDraw2DSVG::drawAtomLabel ( int  atom_num,
const DrawColour draw_colour 
)
overrideprotectedvirtual

Reimplemented from RDKit::MolDraw2D.

◆ drawBond()

void RDKit::MolDraw2DSVG::drawBond ( const ROMol mol,
const Bond bond,
int  at1_idx,
int  at2_idx,
const std::vector< int > *  highlight_atoms = nullptr,
const std::map< int, DrawColour > *  highlight_atom_map = nullptr,
const std::vector< int > *  highlight_bonds = nullptr,
const std::map< int, DrawColour > *  highlight_bond_map = nullptr,
const std::vector< std::pair< DrawColour, DrawColour >> *  bond_colours = nullptr 
)
overrideprotectedvirtual

Reimplemented from RDKit::MolDraw2D.

◆ drawEllipse()

void RDKit::MolDraw2DSVG::drawEllipse ( const Point2D cds1,
const Point2D cds2 
)
overridevirtual

draw an ellipse

Reimplemented from RDKit::MolDraw2D.

◆ drawLine()

void RDKit::MolDraw2DSVG::drawLine ( const Point2D cds1,
const Point2D cds2 
)
overridevirtual

draws a line from cds1 to cds2 using the current drawing style in atom coords.

Implements RDKit::MolDraw2D.

◆ drawPolygon()

void RDKit::MolDraw2DSVG::drawPolygon ( const std::vector< Point2D > &  cds)
overridevirtual

draw a polygon. Note that if fillPolys() returns false, it doesn't close the path. If you want it to in that case, you do it explicitly yourself.

Implements RDKit::MolDraw2D.

◆ drawWavyLine()

void RDKit::MolDraw2DSVG::drawWavyLine ( const Point2D cds1,
const Point2D cds2,
const DrawColour col1,
const DrawColour col2,
unsigned int  nSegments = 16,
double  vertOffset = 0.05 
)
overridevirtual

draw a wavy line like that used to indicate unknown stereochemistry

Reimplemented from RDKit::MolDraw2D.

◆ finishDrawing()

void RDKit::MolDraw2DSVG::finishDrawing ( )

◆ getDrawingText()

std::string RDKit::MolDraw2DSVG::getDrawingText ( ) const
inline

Definition at line 64 of file MolDraw2DSVG.h.

◆ outputClasses()

virtual void RDKit::MolDraw2DSVG::outputClasses ( )
protectedvirtual

◆ setColour()

void RDKit::MolDraw2DSVG::setColour ( const DrawColour col)
overridevirtual

sets the current draw color

Reimplemented from RDKit::MolDraw2D.

◆ tagAtoms() [1/3]

virtual void RDKit::MolDraw2D::tagAtoms
inline

adds additional information about the atoms to the output. Does not make sense for all renderers.

Definition at line 638 of file MolDraw2D.h.

◆ tagAtoms() [2/3]

void RDKit::MolDraw2DSVG::tagAtoms ( const ROMol mol)
inlineoverridevirtual

adds additional information about the atoms to the output. Does not make sense for all renderers.

Reimplemented from RDKit::MolDraw2D.

Definition at line 69 of file MolDraw2DSVG.h.

References tagAtoms().

Referenced by tagAtoms().

◆ tagAtoms() [3/3]

void RDKit::MolDraw2DSVG::tagAtoms ( const ROMol mol,
double  radius,
const std::map< std::string, std::string > &  events = {} 
)

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