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RDKit
Open-source cheminformatics and machine learning.
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MolDraw2D is the base class for doing 2D renderings of molecules. More...
#include <MolDraw2D.h>
Public Member Functions | |
MolDraw2D (int width, int height, int panelWidth, int panelHeight) | |
constructor for a particular size More... | |
virtual | ~MolDraw2D () |
Transformations | |
std::unique_ptr< DrawText > | text_drawer_ |
std::vector< std::pair< std::string, std::string > > | d_metadata |
unsigned int | d_numMetadataEntries = 0 |
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 |
returns the drawing scale (conversion from molecular coords -> drawing More... | |
void | calculateScale (int width, int height, const ROMol &mol, const std::vector< int > *highlight_atoms=nullptr, const std::map< int, double > *highlight_radii=nullptr) |
calculates the drawing scale (conversion from molecular coords -> drawing More... | |
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) |
overload More... | |
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 void | setColour (const DrawColour &col) |
sets the current draw color More... | |
virtual DrawColour | colour () const |
returns the current draw color More... | |
virtual void | setDash (const DashPattern &patt) |
sets the current dash pattern More... | |
virtual const DashPattern & | dash () 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 | drawEllipse (const Point2D &cds1, const Point2D &cds2) |
draw an ellipse More... | |
virtual void | drawArc (const Point2D ¢re, double radius, double ang1, double ang2) |
virtual void | drawArc (const Point2D ¢re, 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 | drawWavyLine (const Point2D &cds1, const Point2D &cds2, const DrawColour &col1, const DrawColour &col2, unsigned int nSegments=16, double vertOffset=0.05) |
draw a wavy line like that used to indicate unknown stereochemistry More... | |
virtual void | tagAtoms (const ROMol &mol) |
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... | |
MolDrawOptions & | drawOptions () |
returns our current drawing options More... | |
const MolDrawOptions & | drawOptions () 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 () |
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 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) |
virtual void | drawAtomLabel (int atom_num, const DrawColour &draw_colour) |
virtual void | drawAnnotation (const std::string ¬e, const std::shared_ptr< StringRect > ¬e_rect) |
Point2D | calcPerpendicular (const Point2D &cds1, const Point2D &cds2) const |
void | calcDoubleBondLines (const ROMol &mol, double offset, const Bond *bond, const Point2D &at1_cds, const Point2D &at2_cds, Point2D &l1s, Point2D &l1f, Point2D &l2s, Point2D &l2f) const |
bool | isLinearAtom (const Atom &atom) const |
void | calcTripleBondLines (double offset, const Bond *bond, const Point2D &at1_cds, const Point2D &at2_cds, Point2D &l1s, Point2D &l1f, Point2D &l2s, Point2D &l2f) const |
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) |
Methods that must be provided by child classes | |
virtual void | clearDrawing ()=0 |
clears the contents of the drawing More... | |
virtual void | drawLine (const Point2D &cds1, const Point2D &cds2)=0 |
draws a line from cds1 to cds2 using the current drawing style More... | |
virtual void | drawPolygon (const std::vector< Point2D > &cds)=0 |
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... | |
MolDraw2D is the base class for doing 2D renderings of molecules.
Definition at line 281 of file MolDraw2D.h.
RDKit::MolDraw2D::MolDraw2D | ( | int | width, |
int | height, | ||
int | panelWidth, | ||
int | panelHeight | ||
) |
constructor for a particular size
width | : width (in pixels) of the rendering |
height | : height (in pixels) of the rendering |
panelWidth | : (optional) width (in pixels) of a single panel |
panelHeight | : (optional) height (in pixels) of a single panel |
The panelWidth
and panelHeight
arguments are used to provide the sizes of the panels individual molecules are drawn in when drawMolecules()
is called.
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returns the coordinates of the atoms of the current molecule in molecular coordinates
Definition at line 591 of file MolDraw2D.h.
References PRECONDITION.
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returns the atomic symbols of the current molecule
Definition at line 596 of file MolDraw2D.h.
References PRECONDITION.
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void RDKit::MolDraw2D::calculateScale | ( | int | width, |
int | height, | ||
const ROMol & | mol, | ||
const std::vector< int > * | highlight_atoms = nullptr , |
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const std::map< int, double > * | highlight_radii = nullptr |
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calculates the drawing scale (conversion from molecular coords -> drawing
void RDKit::MolDraw2D::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 | ||
) |
overload
void RDKit::MolDraw2D::centrePicture | ( | int | width, |
int | height | ||
) |
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clears the contents of the drawing
Implemented in RDKit::MolDraw2DSVG, RDKit::MolDraw2DJS, RDKit::MolDraw2DCairo, RDKit::MolDraw2Dwx, and RDKit::MolDraw2DQt.
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returns the current draw color
Definition at line 515 of file MolDraw2D.h.
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returns the current dash pattern
Definition at line 519 of file MolDraw2D.h.
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Reimplemented in RDKit::MolDraw2DSVG.
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Draw an arrow with either lines or a filled head (when asPolygon is true)
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Reimplemented in RDKit::MolDraw2DSVG.
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draw a line indicating the presence of an attachment point (normally a squiggle line perpendicular to a bond)
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Reimplemented in RDKit::MolDraw2DSVG.
draw an ellipse
Reimplemented in RDKit::MolDraw2DSVG, and RDKit::MolDraw2DJS.
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Definition at line 471 of file MolDraw2D.h.
draws a line from cds1
to cds2
using the current drawing style
Implemented in RDKit::MolDraw2DSVG, RDKit::MolDraw2DJS, RDKit::MolDraw2DCairo, RDKit::MolDraw2Dwx, and RDKit::MolDraw2DQt.
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draw a single molecule
mol | : the molecule to draw |
legend | : the legend (to be drawn under the molecule) |
highlight_atoms | : (optional) vector of atom ids to highlight |
highlight_atoms | : (optional) vector of bond ids to highlight |
highlight_atom_map | : (optional) map from atomId -> DrawColour providing the highlight colors. If not provided the default highlight colour from drawOptions() will be used. |
highlight_bond_map | : (optional) map from bondId -> DrawColour providing the highlight colors. If not provided the default highlight colour from drawOptions() will be used. |
highlight_radii | : (optional) map from atomId -> radius (in molecule coordinates) for the radii of atomic highlights. If not provided the default value from drawOptions() will be used. |
confId | : (optional) conformer ID to be used for atomic coordinates |
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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draw multiple molecules in a grid
mols | : the molecules to draw |
legends | : (optional) the legends (to be drawn under the molecules) |
highlight_atoms | : (optional) vectors of atom ids to highlight |
highlight_atoms | : (optional) vectors of bond ids to highlight |
highlight_atom_map | : (optional) maps from atomId -> DrawColour providing the highlight colors. If not provided the default highlight colour from drawOptions() will be used. |
highlight_bond_map | : (optional) maps from bondId -> DrawColour providing the highlight colors. If not provided the default highlight colour from drawOptions() will be used. |
highlight_radii | : (optional) maps from atomId -> radius (in molecule coordinates) for the radii of atomic highlights. If not provided the default value from drawOptions() will be used. |
confId | : (optional) conformer IDs to be used for atomic coordinates |
The panelWidth
and panelHeight
values will be used to determine the number of rows and columns to be drawn. Theres not a lot of error checking here, so if you provide too many molecules for the number of panes things are likely to get screwed up. If the number of rows or columns ends up being <= 1, molecules will be being drawn in a single row/column.
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draw molecule with multiple colours allowed per atom.
mol | : the molecule to draw |
legend | : the legend (to be drawn under the molecule) |
highlight_atom_map | : map from atomId -> DrawColours providing the highlight colours. |
highlight_bond_map | : map from bondId -> DrawColours providing the highlight colours. |
highlight_radii | : map from atomId -> radius (in molecule coordinates) for the radii of atomic highlights. If not provided for an index, the default value from drawOptions() will be used. |
confId | : (optional) conformer ID to be used for atomic coordinates |
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returns our current drawing options
Definition at line 585 of file MolDraw2D.h.
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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 587 of file MolDraw2D.h.
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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.
Implemented in RDKit::MolDraw2DSVG, RDKit::MolDraw2DJS, RDKit::MolDraw2DCairo, RDKit::MolDraw2Dwx, and RDKit::MolDraw2DQt.
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draw a ChemicalReaction
rxn | : the reaction to draw |
highlightByReactant | : (optional) if this is set, atoms and bonds will be highlighted based on which reactant they come from. Atom map numbers will not be shown. |
highlightColorsReactants | : (optional) provide a vector of colors for the reactant highlighting. |
confIds | : (optional) vector of confIds to use for rendering. These are numbered by reactants, then agents, then products. |
draw a rectangle
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drawString centres the string on cds.
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draw a triangle
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draw a wavy line like that used to indicate unknown stereochemistry
Reimplemented in RDKit::MolDraw2DSVG, and RDKit::MolDraw2DCairo.
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set whether or not polygons are being filled
Definition at line 580 of file MolDraw2D.h.
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font size in drawing coordinate units. That's probably pixels.
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transform a point from drawing coordinates to the molecule coordinate system
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returns the molecular coordinates of a particular atom
transform a point from the molecule coordinate system into the drawing coordinate system
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returns the drawing coordinates of a particular atom
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void RDKit::MolDraw2D::getLabelSize | ( | const std::string & | label, |
OrientType | orient, | ||
double & | label_width, | ||
double & | label_height | ||
) | const |
void RDKit::MolDraw2D::getStringExtremes | ( | const std::string & | label, |
OrientType | orient, | ||
const Point2D & | cds, | ||
double & | x_min, | ||
double & | y_min, | ||
double & | x_max, | ||
double & | y_max | ||
) | const |
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using the current scale, work out the size of the label in molecule coordinates.
Bear in mind when implementing this, that, for example, NH2 will appear as NH2 to convey that the 2 is a subscript, and this needs to accounted for in the width and height.
Reimplemented in RDKit::MolDraw2Dwx.
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return the height of the drawing area.
Definition at line 466 of file MolDraw2D.h.
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returns the current line width
Definition at line 524 of file MolDraw2D.h.
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returns the minimum point of the drawing (in molecular coords)
Definition at line 504 of file MolDraw2D.h.
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returns the drawing offset (in drawing coords)
Definition at line 501 of file MolDraw2D.h.
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return the height of the drawing panels.
Definition at line 470 of file MolDraw2D.h.
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return the width of the drawing panels.
Definition at line 468 of file MolDraw2D.h.
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returns the width and height of the grid (in molecular coords)
Definition at line 506 of file MolDraw2D.h.
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returns the drawing scale (conversion from molecular coords -> drawing
Definition at line 475 of file MolDraw2D.h.
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sets the current draw color
Reimplemented in RDKit::MolDraw2DSVG, RDKit::MolDraw2DCairo, RDKit::MolDraw2Dwx, and RDKit::MolDraw2DQt.
Definition at line 513 of file MolDraw2D.h.
Referenced by RDKit::MolDraw2Dwx::setColour().
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sets the current dash pattern
Definition at line 517 of file MolDraw2D.h.
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returns either or not polygons should be filled
Definition at line 582 of file MolDraw2D.h.
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Reimplemented in RDKit::MolDraw2Dwx.
Referenced by RDKit::MolDraw2Dwx::setFontSize().
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sets the current line width
Definition at line 522 of file MolDraw2D.h.
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sets the drawing offset (in drawing coords)
Definition at line 496 of file MolDraw2D.h.
void RDKit::MolDraw2D::setScale | ( | int | width, |
int | height, | ||
const Point2D & | minv, | ||
const Point2D & | maxv, | ||
const ROMol * | mol = nullptr |
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explicitly sets the scaling factors for the drawing
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Definition at line 608 of file MolDraw2D.h.
void RDKit::MolDraw2D::tabulaRasa | ( | ) |
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adds additional information about the atoms to the output. Does not make sense for all renderers.
Reimplemented in RDKit::MolDraw2DSVG.
Definition at line 578 of file MolDraw2D.h.
References RDUNUSED_PARAM.
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return the width of the drawing area.
Definition at line 464 of file MolDraw2D.h.
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Definition at line 810 of file MolDraw2D.h.
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Definition at line 811 of file MolDraw2D.h.
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Definition at line 611 of file MolDraw2D.h.